Command-line options
Command line interface for stdpopsim.
usage: stdpopsim [-h] [-V] [-v | -q] [-c CACHE_DIR] [-e {msprime,slim}]
[--msprime-model {hudson,dtwf,smc,smc_prime}]
[--msprime-change-model T MODEL] [--slim-path PATH]
[--slim-script] [--slim-scaling-factor Q] [--slim-burn-in X]
{AedAeg,AnaPla,AnoCar,AnoGam,ApiMel,AraTha,BosTau,CaeEle,CanFam,ChlRei,DroMel,DroSec,EscCol,GasAcu,GorGor,HelAnn,HelMel,HomSap,MusMus,OrySat,PanTro,PapAnu,PhoSin,PonAbe,RatNor,StrAga,SusScr,download-genetic-maps}
...
Positional Arguments
- subcommand
Possible choices: AedAeg, AnaPla, AnoCar, AnoGam, ApiMel, AraTha, BosTau, CaeEle, CanFam, ChlRei, DroMel, DroSec, EscCol, GasAcu, GorGor, HelAnn, HelMel, HomSap, MusMus, OrySat, PanTro, PapAnu, PhoSin, PonAbe, RatNor, StrAga, SusScr, download-genetic-maps
Named Arguments
- -V, --version
show program’s version number and exit
- -v, --verbose
Increase logging verbosity (can use be used multiple times).
Default:
1- -q, --quiet
Do not write any non-essential messages
- -c, --cache-dir
Set the cache directory to the specified value. Note that this can also be set using the environment variable STDPOPSIM_CACHE. If both the environment variable and this option are set, the option takes precedence. Default: /home/runner/.cache/stdpopsim
- -e, --engine
Possible choices: msprime, slim
Specify a simulation engine.
Default:
'msprime'
msprime specific parameters
- --msprime-model
Possible choices: hudson, dtwf, smc, smc_prime
Specify the simulation model used by msprime. See msprime API documentation for details.
Default:
'hudson'- --msprime-change-model
Change to the specified simulation MODEL at generation T. This option may provided multiple times.
Default:
[]
SLiM specific parameters
- --slim-path
Full path to `slim’ executable.
- --slim-script
Write script to stdout and exit without running SLiM.
Default:
False- --slim-scaling-factor
Rescale model parameters by Q to speed up simulation. See SLiM manual: 5.5 Rescaling population sizes to improve simulation performance. [default=1].
Default:
1- --slim-burn-in
Length of the burn-in phase, in units of N generations [default=10].
Default:
10
Sub-commands
AedAeg
Run simulations for Aedes aegypti using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘–output’ option to specify a filename.
Default population parameters for Aedes aegypti: Generation time: 0.06666666666666667 Population size: 1000000.0 Mutation rate: 3.5e-09 Recombination rate: 2.782e-09
stdpopsim AedAeg [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D] [-c]
[-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
[-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
[-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
[--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
samples [samples ...]
Positional Arguments
- samples
The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.
Named Arguments
- --help-models
Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models
- -b, --bibtex-file
Write citations to a given bib file. This will overwrite the file.
- -D, --dry-run
Do not run actual simulation
Default:
False- -c, --chromosome
Possible choices: 1, chr1, 2, chr2, 3, chr3, MT, chrM
Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, MT. Default=None.
- -L, --length
Simulate a default contig of given length.
- -i, --inclusion-mask
Path to inclusion mask specified in bed format.
- -e, --exclusion-mask
Path to exclusion mask specified in bed format.
- -l, --length-multiplier
Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.
- --left
The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).
- --right
The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.
- -s, --seed
The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.
- --keep-mutation-ids-as-alleles
If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.
Default:
False- -d, --demographic-model
Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: . Please see –help-models for details of these models.
- --dfe
Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.
- --dfe-interval
Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.
- --dfe-bed-file
A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.
- -o, --output
Where to write the output tree sequence file. Defaults to stdout if not specified
AnaPla
Run simulations for Anas platyrhynchos using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.
Default population parameters for Anas platyrhynchos: Generation time: 4 Population size: 156000 Mutation rate: 4.83e-09 Recombination rate: 1.433e-08
stdpopsim AnaPla [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D] [-c]
[-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
[-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
[-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
[--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
samples [samples ...]
Positional Arguments
- samples
The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.
Named Arguments
- --help-models
Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models
- -b, --bibtex-file
Write citations to a given bib file. This will overwrite the file.
- -D, --dry-run
Do not run actual simulation
Default:
False- -c, --chromosome
Possible choices: 1, chr1, 2, chr2, 3, chr3, 4, chr4, 5, chr5, 6, chr6, 7, chr7, 8, chr8, 9, chr9, 10, chr10, 11, chr11, 12, chr12, 13, chr13, 14, chr14, 15, chr15, 16, chr16, 17, chr17, 18, chr18, 19, chr19, 20, chr20, 21, chr21, 22, chr22, 23, chr23, 24, chr24, 25, chr25, 26, chr26, 27, chr27, 28, chr28, 29, chr29, 30, chr30, Z, chrZ, 31, chr31, 32, chr32, 33, chr33, 34, chr34, 35, chr35, 36, chr36, 37, chr37, 38, chr38, 39, chr39, 40, chr40
Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, Z, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40. Default=None.
- -L, --length
Simulate a default contig of given length.
- -i, --inclusion-mask
Path to inclusion mask specified in bed format.
- -e, --exclusion-mask
Path to exclusion mask specified in bed format.
- -l, --length-multiplier
Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.
- --left
The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).
- --right
The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.
- -s, --seed
The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.
- --keep-mutation-ids-as-alleles
If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.
Default:
False- -d, --demographic-model
Possible choices: MallardBlackDuck_2L19
Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: MallardBlackDuck_2L19. Please see –help-models for details of these models.
- --dfe
Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.
- --dfe-interval
Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.
- --dfe-bed-file
A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.
- -o, --output
Where to write the output tree sequence file. Defaults to stdout if not specified
AnoCar
Run simulations for Anolis carolinensis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.
Default population parameters for Anolis carolinensis: Generation time: 1.5 Population size: 3050000.0 Mutation rate: 2.1e-10 Recombination rate: 1.59e-08
stdpopsim AnoCar [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D] [-c]
[-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
[-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
[-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
[--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
samples [samples ...]
Positional Arguments
- samples
The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.
Named Arguments
- --help-models
Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models
- -b, --bibtex-file
Write citations to a given bib file. This will overwrite the file.
- -D, --dry-run
Do not run actual simulation
Default:
False- -c, --chromosome
Possible choices: 1, chr1, 2, chr2, 3, chr3, 4, chr4, 5, chr5, 6, chr6, LGa, LGb, LGc, LGd, LGf, LGg, LGh, MT, chrM
Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, LGa, LGb, LGc, LGd, LGf, LGg, LGh, MT. Default=None.
- -L, --length
Simulate a default contig of given length.
- -i, --inclusion-mask
Path to inclusion mask specified in bed format.
- -e, --exclusion-mask
Path to exclusion mask specified in bed format.
- -l, --length-multiplier
Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.
- --left
The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).
- --right
The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.
- -s, --seed
The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.
- --keep-mutation-ids-as-alleles
If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.
Default:
False- -d, --demographic-model
Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: . Please see –help-models for details of these models.
- --dfe
Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.
- --dfe-interval
Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.
- --dfe-bed-file
A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.
- -o, --output
Where to write the output tree sequence file. Defaults to stdout if not specified
AnoGam
Run simulations for Anopheles gambiae using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.
Default population parameters for Anopheles gambiae: Generation time: 0.09090909090909091 Population size: 1000000.0 Mutation rate: 3.5e-09 Recombination rate: 1.447e-08
stdpopsim AnoGam [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D] [-c]
[-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
[-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
[-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
[--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
samples [samples ...]
Positional Arguments
- samples
The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.
Named Arguments
- --help-models
Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models
- -b, --bibtex-file
Write citations to a given bib file. This will overwrite the file.
- -D, --dry-run
Do not run actual simulation
Default:
False- -c, --chromosome
Possible choices: 2L, chr2L, 2R, chr2R, 3L, chr3L, 3R, chr3R, X, chrX, Mt
Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 2L, 2R, 3L, 3R, X, Mt. Default=None.
- -L, --length
Simulate a default contig of given length.
- -i, --inclusion-mask
Path to inclusion mask specified in bed format.
- -e, --exclusion-mask
Path to exclusion mask specified in bed format.
- -l, --length-multiplier
Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.
- --left
The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).
- --right
The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.
- -s, --seed
The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.
- --keep-mutation-ids-as-alleles
If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.
Default:
False- -d, --demographic-model
Possible choices: GabonAg1000G_1A17
Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: GabonAg1000G_1A17. Please see –help-models for details of these models.
- --dfe
Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.
- --dfe-interval
Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.
- --dfe-bed-file
A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.
- -o, --output
Where to write the output tree sequence file. Defaults to stdout if not specified
ApiMel
Run simulations for Apis mellifera using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.
Default population parameters for Apis mellifera: Generation time: 2 Population size: 200000.0 Mutation rate: 3.4e-09 Recombination rate: 2.318e-07
stdpopsim ApiMel [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D] [-c]
[-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
[-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
[-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
[--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
samples [samples ...]
Positional Arguments
- samples
The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.
Named Arguments
- --help-models
Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models
- -b, --bibtex-file
Write citations to a given bib file. This will overwrite the file.
- -D, --dry-run
Do not run actual simulation
Default:
False- -c, --chromosome
Possible choices: CM009931.2, NC_037638.1, 1, CM009932.2, NC_037639.1, 2, CM009933.2, 3, NC_037640.1, CM009934.2, NC_037641.1, 4, CM009935.2, 5, NC_037642.1, CM009936.2, NC_037643.1, 6, CM009937.2, NC_037644.1, 7, CM009938.2, NC_037645.1, 8, CM009939.2, 9, NC_037646.1, CM009940.2, 10, NC_037647.1, CM009941.2, 11, NC_037648.1, CM009942.2, NC_037649.1, 12, CM009943.2, NC_037650.1, 13, CM009944.2, 14, NC_037651.1, CM009945.2, NC_037652.1, 15, CM009946.2, 16, NC_037653.1, CM009947.2, NC_001566.1, MT
Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: CM009931.2, CM009932.2, CM009933.2, CM009934.2, CM009935.2, CM009936.2, CM009937.2, CM009938.2, CM009939.2, CM009940.2, CM009941.2, CM009942.2, CM009943.2, CM009944.2, CM009945.2, CM009946.2, CM009947.2. Default=None.
- -L, --length
Simulate a default contig of given length.
- -i, --inclusion-mask
Path to inclusion mask specified in bed format.
- -e, --exclusion-mask
Path to exclusion mask specified in bed format.
- -l, --length-multiplier
Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.
- --left
The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).
- --right
The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.
- -s, --seed
The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.
- --keep-mutation-ids-as-alleles
If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.
Default:
False- -d, --demographic-model
Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: . Please see –help-models for details of these models.
- --dfe
Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.
- --dfe-interval
Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.
- --dfe-bed-file
A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.
- -o, --output
Where to write the output tree sequence file. Defaults to stdout if not specified
AraTha
Run simulations for Arabidopsis thaliana using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.
Default population parameters for Arabidopsis thaliana: Generation time: 1.0 Population size: 10000 Mutation rate: 7e-09 Recombination rate: 8.029e-10
stdpopsim AraTha [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE]
[--help-genetic-maps [HELP_GENETIC_MAPS]] [-D] [-g]
[--help-dfes [HELP_DFES]] [-c] [-L LENGTH]
[-i INCLUSION_MASK] [-e EXCLUSION_MASK]
[-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
[-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
[--dfe-interval] [--dfe-bed-file]
[--help-annotations [HELP_ANNOTATIONS]] [--dfe-annotation]
[-o OUTPUT]
samples [samples ...]
Positional Arguments
- samples
The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.
Named Arguments
- --help-models
Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models
- -b, --bibtex-file
Write citations to a given bib file. This will overwrite the file.
- --help-genetic-maps
Print list of genetic maps and exit. If a genetic map ID is given as an argument, show help for this map. Otherwise show help for all available genetic maps
- -D, --dry-run
Do not run actual simulation
Default:
False- -g, --genetic-map
Possible choices: SalomeAveraged_TAIR10
Specify a particular genetic map. By default, a chromosome-specific uniform recombination rate is used. These default rates are listed in the catalog: <https://popsim-consortium.github.io/stdpopsim-docs/stable/catalog.html> Available maps: SalomeAveraged_TAIR10.
- --help-dfes
Print list of DFEs and exit. If a DFE ID is given as an argument, show help for this DFE. Otherwise show help for all available DFEs
- -c, --chromosome
Possible choices: 1, chr1, 2, chr2, 3, chr3, 4, chr4, 5, chr5, Mt, Pt
Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, Mt, Pt. Default=None.
- -L, --length
Simulate a default contig of given length.
- -i, --inclusion-mask
Path to inclusion mask specified in bed format.
- -e, --exclusion-mask
Path to exclusion mask specified in bed format.
- -l, --length-multiplier
Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.
- --left
The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).
- --right
The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.
- -s, --seed
The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.
- --keep-mutation-ids-as-alleles
If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.
Default:
False- -d, --demographic-model
Possible choices: SouthMiddleAtlas_1D17, African2Epoch_1H18, African3Epoch_1H18
Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: SouthMiddleAtlas_1D17, African2Epoch_1H18, African3Epoch_1H18. Please see –help-models for details of these models.
- --dfe
Possible choices: GammaAdditive_H18
Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:GammaAdditive_H18. Please see –help-dfes for details of these DFE models.
- --dfe-interval
Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.
- --dfe-bed-file
A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.
- --help-annotations
Print list of annotations and exit. If a annotation ID is given as an argument, show help for this annotation. Otherwise show help for all available annotations
- --dfe-annotation
Possible choices: araport_11_exons, araport_11_CDS
Specify the intervals over which a given DFE acts using a genomic annotation track Available maps: araport_11_exons, araport_11_CDS.
- -o, --output
Where to write the output tree sequence file. Defaults to stdout if not specified
BosTau
Run simulations for Bos taurus using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘–output’ option to specify a filename.
Default population parameters for Bos taurus: Generation time: 5 Population size: 62000 Mutation rate: 1.2e-08 Recombination rate: 9.26e-09
stdpopsim BosTau [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D] [-c]
[-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
[-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
[-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
[--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
samples [samples ...]
Positional Arguments
- samples
The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.
Named Arguments
- --help-models
Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models
- -b, --bibtex-file
Write citations to a given bib file. This will overwrite the file.
- -D, --dry-run
Do not run actual simulation
Default:
False- -c, --chromosome
Possible choices: 1, chr1, 2, chr2, 3, chr3, 4, chr4, 5, chr5, 6, chr6, 7, chr7, 8, chr8, 9, chr9, 10, chr10, 11, chr11, 12, chr12, 13, chr13, 14, chr14, 15, chr15, 16, chr16, 17, chr17, 18, chr18, 19, chr19, 20, chr20, 21, chr21, 22, chr22, 23, chr23, 24, chr24, 25, chr25, 26, chr26, 27, chr27, 28, chr28, 29, chr29, X, chrX, MT, chrM
Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, X, MT. Default=None.
- -L, --length
Simulate a default contig of given length.
- -i, --inclusion-mask
Path to inclusion mask specified in bed format.
- -e, --exclusion-mask
Path to exclusion mask specified in bed format.
- -l, --length-multiplier
Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.
- --left
The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).
- --right
The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.
- -s, --seed
The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.
- --keep-mutation-ids-as-alleles
If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.
Default:
False- -d, --demographic-model
Possible choices: HolsteinFriesian_1M13, HolsteinFriesian_1B16, Fleckvieh_1B16, Jersey_1B16, Angus_1B16
Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: HolsteinFriesian_1M13, HolsteinFriesian_1B16, Fleckvieh_1B16, Jersey_1B16, Angus_1B16. Please see –help-models for details of these models.
- --dfe
Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.
- --dfe-interval
Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.
- --dfe-bed-file
A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.
- -o, --output
Where to write the output tree sequence file. Defaults to stdout if not specified
CaeEle
Run simulations for Caenorhabditis elegans using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.
Default population parameters for Caenorhabditis elegans: Generation time: 0.01 Population size: 10000 Mutation rate: 1.854e-09 Recombination rate: 3.053e-11
stdpopsim CaeEle [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE]
[--help-genetic-maps [HELP_GENETIC_MAPS]] [-D] [-g] [-c]
[-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
[-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
[-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
[--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
samples [samples ...]
Positional Arguments
- samples
The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.
Named Arguments
- --help-models
Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models
- -b, --bibtex-file
Write citations to a given bib file. This will overwrite the file.
- --help-genetic-maps
Print list of genetic maps and exit. If a genetic map ID is given as an argument, show help for this map. Otherwise show help for all available genetic maps
- -D, --dry-run
Do not run actual simulation
Default:
False- -g, --genetic-map
Possible choices: RockmanRIAIL_ce11
Specify a particular genetic map. By default, a chromosome-specific uniform recombination rate is used. These default rates are listed in the catalog: <https://popsim-consortium.github.io/stdpopsim-docs/stable/catalog.html> Available maps: RockmanRIAIL_ce11.
- -c, --chromosome
Possible choices: I, II, III, IV, V, X, MtDNA
Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: I, II, III, IV, V, X, MtDNA. Default=None.
- -L, --length
Simulate a default contig of given length.
- -i, --inclusion-mask
Path to inclusion mask specified in bed format.
- -e, --exclusion-mask
Path to exclusion mask specified in bed format.
- -l, --length-multiplier
Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.
- --left
The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).
- --right
The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.
- -s, --seed
The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.
- --keep-mutation-ids-as-alleles
If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.
Default:
False- -d, --demographic-model
Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: . Please see –help-models for details of these models.
- --dfe
Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.
- --dfe-interval
Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.
- --dfe-bed-file
A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.
- -o, --output
Where to write the output tree sequence file. Defaults to stdout if not specified
CanFam
Run simulations for Canis familiaris using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.
Default population parameters for Canis familiaris: Generation time: 3 Population size: 13000 Mutation rate: 4e-09 Recombination rate: 9.506e-09
stdpopsim CanFam [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE]
[--help-genetic-maps [HELP_GENETIC_MAPS]] [-D] [-g] [-c]
[-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
[-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
[-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
[--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
samples [samples ...]
Positional Arguments
- samples
The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.
Named Arguments
- --help-models
Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models
- -b, --bibtex-file
Write citations to a given bib file. This will overwrite the file.
- --help-genetic-maps
Print list of genetic maps and exit. If a genetic map ID is given as an argument, show help for this map. Otherwise show help for all available genetic maps
- -D, --dry-run
Do not run actual simulation
Default:
False- -g, --genetic-map
Possible choices: Campbell2016_CanFam3_1
Specify a particular genetic map. By default, a chromosome-specific uniform recombination rate is used. These default rates are listed in the catalog: <https://popsim-consortium.github.io/stdpopsim-docs/stable/catalog.html> Available maps: Campbell2016_CanFam3_1.
- -c, --chromosome
Possible choices: 1, chr1, 2, chr2, 3, chr3, 4, chr4, 5, chr5, 6, chr6, 7, chr7, 8, chr8, 9, chr9, 10, chr10, 11, chr11, 12, chr12, 13, chr13, 14, chr14, 15, chr15, 16, chr16, 17, chr17, 18, chr18, 19, chr19, 20, chr20, 21, chr21, 22, chr22, 23, chr23, 24, chr24, 25, chr25, 26, chr26, 27, chr27, 28, chr28, 29, chr29, 30, chr30, 31, chr31, 32, chr32, 33, chr33, 34, chr34, 35, chr35, 36, chr36, 37, chr37, 38, chr38, X, chrX, MT, chrM
Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, X, MT. Default=None.
- -L, --length
Simulate a default contig of given length.
- -i, --inclusion-mask
Path to inclusion mask specified in bed format.
- -e, --exclusion-mask
Path to exclusion mask specified in bed format.
- -l, --length-multiplier
Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.
- --left
The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).
- --right
The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.
- -s, --seed
The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.
- --keep-mutation-ids-as-alleles
If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.
Default:
False- -d, --demographic-model
Possible choices: EarlyWolfAdmixture_6F14
Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: EarlyWolfAdmixture_6F14. Please see –help-models for details of these models.
- --dfe
Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.
- --dfe-interval
Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.
- --dfe-bed-file
A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.
- -o, --output
Where to write the output tree sequence file. Defaults to stdout if not specified
ChlRei
Run simulations for Chlamydomonas reinhardtii using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.
Default population parameters for Chlamydomonas reinhardtii: Generation time: 0.001141552511415525 Population size: 1.3999999999999998e-07 Mutation rate: 9.351e-10 Recombination rate: 1.459e-10
stdpopsim ChlRei [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D] [-c]
[-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
[-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
[-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
[--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
samples [samples ...]
Positional Arguments
- samples
The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.
Named Arguments
- --help-models
Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models
- -b, --bibtex-file
Write citations to a given bib file. This will overwrite the file.
- -D, --dry-run
Do not run actual simulation
Default:
False- -c, --chromosome
Possible choices: 1, chr1, 2, chr2, 3, chr3, 4, chr4, 5, chr5, 6, chr6, 7, chr7, 8, chr8, 9, chr9, 10, chr10, 11, chr11, 12, chr12, 13, chr13, 14, chr14, 15, chr15, 16, chr16, 17, chr17
Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17. Default=None.
- -L, --length
Simulate a default contig of given length.
- -i, --inclusion-mask
Path to inclusion mask specified in bed format.
- -e, --exclusion-mask
Path to exclusion mask specified in bed format.
- -l, --length-multiplier
Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.
- --left
The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).
- --right
The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.
- -s, --seed
The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.
- --keep-mutation-ids-as-alleles
If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.
Default:
False- -d, --demographic-model
Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: . Please see –help-models for details of these models.
- --dfe
Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.
- --dfe-interval
Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.
- --dfe-bed-file
A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.
- -o, --output
Where to write the output tree sequence file. Defaults to stdout if not specified
DroMel
Run simulations for Drosophila melanogaster using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.
Default population parameters for Drosophila melanogaster: Generation time: 0.1 Population size: 1720600 Mutation rate: 5.49e-09 Recombination rate: 2.085e-08
stdpopsim DroMel [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE]
[--help-genetic-maps [HELP_GENETIC_MAPS]] [-D] [-g]
[--help-dfes [HELP_DFES]] [-c] [-L LENGTH]
[-i INCLUSION_MASK] [-e EXCLUSION_MASK]
[-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
[-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
[--dfe-interval] [--dfe-bed-file]
[--help-annotations [HELP_ANNOTATIONS]] [--dfe-annotation]
[-o OUTPUT]
samples [samples ...]
Positional Arguments
- samples
The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.
Named Arguments
- --help-models
Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models
- -b, --bibtex-file
Write citations to a given bib file. This will overwrite the file.
- --help-genetic-maps
Print list of genetic maps and exit. If a genetic map ID is given as an argument, show help for this map. Otherwise show help for all available genetic maps
- -D, --dry-run
Do not run actual simulation
Default:
False- -g, --genetic-map
Possible choices: ComeronCrossover_dm6, ComeronCrossoverV2_dm6
Specify a particular genetic map. By default, a chromosome-specific uniform recombination rate is used. These default rates are listed in the catalog: <https://popsim-consortium.github.io/stdpopsim-docs/stable/catalog.html> Available maps: ComeronCrossover_dm6, ComeronCrossoverV2_dm6.
- --help-dfes
Print list of DFEs and exit. If a DFE ID is given as an argument, show help for this DFE. Otherwise show help for all available DFEs
- -c, --chromosome
Possible choices: 2L, chr2L, 2R, chr2R, 3L, chr3L, 3R, chr3R, 4, chr4, X, chrX, Y, chrY, mitochondrion_genome
Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 2L, 2R, 3L, 3R, 4, X, Y, mitochondrion_genome. Default=None.
- -L, --length
Simulate a default contig of given length.
- -i, --inclusion-mask
Path to inclusion mask specified in bed format.
- -e, --exclusion-mask
Path to exclusion mask specified in bed format.
- -l, --length-multiplier
Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.
- --left
The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).
- --right
The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.
- -s, --seed
The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.
- --keep-mutation-ids-as-alleles
If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.
Default:
False- -d, --demographic-model
Possible choices: African3Epoch_1S16, OutOfAfrica_2L06
Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: African3Epoch_1S16, OutOfAfrica_2L06. Please see –help-models for details of these models.
- --dfe
Possible choices: Gamma_H17, GammaPos_H17, LognormalPlusPositive_R16
Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:Gamma_H17, GammaPos_H17, LognormalPlusPositive_R16. Please see –help-dfes for details of these DFE models.
- --dfe-interval
Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.
- --dfe-bed-file
A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.
- --help-annotations
Print list of annotations and exit. If a annotation ID is given as an argument, show help for this annotation. Otherwise show help for all available annotations
- --dfe-annotation
Possible choices: FlyBase_BDGP6.32.51_exons, FlyBase_BDGP6.32.51_CDS
Specify the intervals over which a given DFE acts using a genomic annotation track Available maps: FlyBase_BDGP6.32.51_exons, FlyBase_BDGP6.32.51_CDS.
- -o, --output
Where to write the output tree sequence file. Defaults to stdout if not specified
DroSec
Run simulations for Drosophila sechellia using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.
Default population parameters for Drosophila sechellia: Generation time: 0.05 Population size: 100000 Mutation rate: 1.5e-09 Recombination rate: 2.223e-08
stdpopsim DroSec [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D] [-c]
[-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
[-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
[-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
[--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
samples [samples ...]
Positional Arguments
- samples
The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.
Named Arguments
- --help-models
Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models
- -b, --bibtex-file
Write citations to a given bib file. This will overwrite the file.
- -D, --dry-run
Do not run actual simulation
Default:
False- -c, --chromosome
Possible choices: 2L, chr2L, 2R, chr2R, 3L, chr3L, 3R, chr3R, X, chrX, 4, chr4
Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 2L, 2R, 3L, 3R, X, 4. Default=None.
- -L, --length
Simulate a default contig of given length.
- -i, --inclusion-mask
Path to inclusion mask specified in bed format.
- -e, --exclusion-mask
Path to exclusion mask specified in bed format.
- -l, --length-multiplier
Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.
- --left
The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).
- --right
The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.
- -s, --seed
The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.
- --keep-mutation-ids-as-alleles
If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.
Default:
False- -d, --demographic-model
Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: . Please see –help-models for details of these models.
- --dfe
Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.
- --dfe-interval
Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.
- --dfe-bed-file
A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.
- -o, --output
Where to write the output tree sequence file. Defaults to stdout if not specified
EscCol
Run simulations for Escherichia coli using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.
Default population parameters for Escherichia coli: Generation time: 3.805175e-05 Population size: 180000000.0 Mutation rate: 8.9e-11 Recombination rate: 8.9e-11 Bacterial recombination with tract length: 542
stdpopsim EscCol [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D] [-c]
[-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
[-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
[-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
[--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
samples [samples ...]
Positional Arguments
- samples
The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.
Named Arguments
- --help-models
Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models
- -b, --bibtex-file
Write citations to a given bib file. This will overwrite the file.
- -D, --dry-run
Do not run actual simulation
Default:
False- -c, --chromosome
Possible choices: Chromosome
Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: Chromosome. Default=None.
- -L, --length
Simulate a default contig of given length.
- -i, --inclusion-mask
Path to inclusion mask specified in bed format.
- -e, --exclusion-mask
Path to exclusion mask specified in bed format.
- -l, --length-multiplier
Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.
- --left
The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).
- --right
The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.
- -s, --seed
The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.
- --keep-mutation-ids-as-alleles
If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.
Default:
False- -d, --demographic-model
Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: . Please see –help-models for details of these models.
- --dfe
Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.
- --dfe-interval
Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.
- --dfe-bed-file
A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.
- -o, --output
Where to write the output tree sequence file. Defaults to stdout if not specified
GasAcu
Run simulations for Gasterosteus aculeatus using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.
Default population parameters for Gasterosteus aculeatus: Generation time: 2 Population size: 10000.0 Mutation rate: 3.7e-08 Recombination rate: 3.001e-08
stdpopsim GasAcu [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D] [-c]
[-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
[-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
[-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
[--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
samples [samples ...]
Positional Arguments
- samples
The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.
Named Arguments
- --help-models
Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models
- -b, --bibtex-file
Write citations to a given bib file. This will overwrite the file.
- -D, --dry-run
Do not run actual simulation
Default:
False- -c, --chromosome
Possible choices: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, Y, MT
Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, Y, MT. Default=None.
- -L, --length
Simulate a default contig of given length.
- -i, --inclusion-mask
Path to inclusion mask specified in bed format.
- -e, --exclusion-mask
Path to exclusion mask specified in bed format.
- -l, --length-multiplier
Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.
- --left
The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).
- --right
The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.
- -s, --seed
The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.
- --keep-mutation-ids-as-alleles
If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.
Default:
False- -d, --demographic-model
Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: . Please see –help-models for details of these models.
- --dfe
Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.
- --dfe-interval
Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.
- --dfe-bed-file
A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.
- -o, --output
Where to write the output tree sequence file. Defaults to stdout if not specified
GorGor
Run simulations for Gorilla gorilla using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.
Default population parameters for Gorilla gorilla: Generation time: 19.0 Population size: 25200 Mutation rate: 1.235e-08 Recombination rate: 1.193e-08
stdpopsim GorGor [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D] [-c]
[-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
[-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
[-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
[--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
samples [samples ...]
Positional Arguments
- samples
The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.
Named Arguments
- --help-models
Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models
- -b, --bibtex-file
Write citations to a given bib file. This will overwrite the file.
- -D, --dry-run
Do not run actual simulation
Default:
False- -c, --chromosome
Possible choices: 1, chr1, 2A, chr2A, 2B, chr2B, 3, chr3, 4, chr4, 5, chr5, 6, chr6, 7, chr7, 8, chr8, 9, chr9, 10, chr10, 11, chr11, 12, chr12, 13, chr13, 14, chr14, 15, chr15, 16, chr16, 17, chr17, 18, chr18, 19, chr19, 20, chr20, 21, chr21, 22, chr22, X, chrX, MT, chrM
Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2A, 2B, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, MT. Default=None.
- -L, --length
Simulate a default contig of given length.
- -i, --inclusion-mask
Path to inclusion mask specified in bed format.
- -e, --exclusion-mask
Path to exclusion mask specified in bed format.
- -l, --length-multiplier
Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.
- --left
The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).
- --right
The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.
- -s, --seed
The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.
- --keep-mutation-ids-as-alleles
If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.
Default:
False- -d, --demographic-model
Possible choices: GorillaGhost_5P23
Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: GorillaGhost_5P23. Please see –help-models for details of these models.
- --dfe
Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.
- --dfe-interval
Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.
- --dfe-bed-file
A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.
- -o, --output
Where to write the output tree sequence file. Defaults to stdout if not specified
HelAnn
Run simulations for Helianthus annuus using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.
Default population parameters for Helianthus annuus: Generation time: 1.0 Population size: 673968 Mutation rate: 6.1e-09 Recombination rate: 4e-09
stdpopsim HelAnn [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D] [-c]
[-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
[-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
[-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
[--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
samples [samples ...]
Positional Arguments
- samples
The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.
Named Arguments
- --help-models
Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models
- -b, --bibtex-file
Write citations to a given bib file. This will overwrite the file.
- -D, --dry-run
Do not run actual simulation
Default:
False- -c, --chromosome
Possible choices: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17
Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17. Default=None.
- -L, --length
Simulate a default contig of given length.
- -i, --inclusion-mask
Path to inclusion mask specified in bed format.
- -e, --exclusion-mask
Path to exclusion mask specified in bed format.
- -l, --length-multiplier
Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.
- --left
The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).
- --right
The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.
- -s, --seed
The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.
- --keep-mutation-ids-as-alleles
If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.
Default:
False- -d, --demographic-model
Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: . Please see –help-models for details of these models.
- --dfe
Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.
- --dfe-interval
Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.
- --dfe-bed-file
A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.
- -o, --output
Where to write the output tree sequence file. Defaults to stdout if not specified
HelMel
Run simulations for Heliconius melpomene using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.
Default population parameters for Heliconius melpomene: Generation time: 0.0958904109589041 Population size: 2111109 Mutation rate: 2.9e-09 Recombination rate: 3.966e-08
stdpopsim HelMel [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D] [-c]
[-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
[-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
[-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
[--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
samples [samples ...]
Positional Arguments
- samples
The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.
Named Arguments
- --help-models
Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models
- -b, --bibtex-file
Write citations to a given bib file. This will overwrite the file.
- -D, --dry-run
Do not run actual simulation
Default:
False- -c, --chromosome
Possible choices: 1, chr1, 2, chr2, 3, chr3, 4, chr4, 5, chr5, 6, chr6, 7, chr7, 8, chr8, 9, chr9, 10, chr10, 11, chr11, 12, chr12, 13, chr13, 14, chr14, 15, chr15, 16, chr16, 17, chr17, 18, chr18, 19, chr19, 20, chr20, 21, chr21
Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21. Default=None.
- -L, --length
Simulate a default contig of given length.
- -i, --inclusion-mask
Path to inclusion mask specified in bed format.
- -e, --exclusion-mask
Path to exclusion mask specified in bed format.
- -l, --length-multiplier
Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.
- --left
The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).
- --right
The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.
- -s, --seed
The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.
- --keep-mutation-ids-as-alleles
If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.
Default:
False- -d, --demographic-model
Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: . Please see –help-models for details of these models.
- --dfe
Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.
- --dfe-interval
Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.
- --dfe-bed-file
A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.
- -o, --output
Where to write the output tree sequence file. Defaults to stdout if not specified
HomSap
Run simulations for Homo sapiens using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘–output’ option to specify a filename.
Default population parameters for Homo sapiens: Generation time: 30 Population size: 10000 Mutation rate: 1.29e-08 Recombination rate: 1.253e-08
stdpopsim HomSap [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE]
[--help-genetic-maps [HELP_GENETIC_MAPS]] [-D] [-g]
[--help-dfes [HELP_DFES]] [-c] [-L LENGTH]
[-i INCLUSION_MASK] [-e EXCLUSION_MASK]
[-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
[-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
[--dfe-interval] [--dfe-bed-file]
[--help-annotations [HELP_ANNOTATIONS]] [--dfe-annotation]
[-o OUTPUT]
samples [samples ...]
Positional Arguments
- samples
The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.
Named Arguments
- --help-models
Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models
- -b, --bibtex-file
Write citations to a given bib file. This will overwrite the file.
- --help-genetic-maps
Print list of genetic maps and exit. If a genetic map ID is given as an argument, show help for this map. Otherwise show help for all available genetic maps
- -D, --dry-run
Do not run actual simulation
Default:
False- -g, --genetic-map
Possible choices: HapMapII_GRCh37, HapMapII_GRCh38, DeCodeSexAveraged_GRCh36, DeCodeSexAveraged_GRCh38, PyrhoACB_GRCh38, PyrhoASW_GRCh38, PyrhoBEB_GRCh38, PyrhoCDX_GRCh38, PyrhoCEU_GRCh38, PyrhoCHB_GRCh38, PyrhoCHS_GRCh38, PyrhoCLM_GRCh38, PyrhoESN_GRCh38, PyrhoFIN_GRCh38, PyrhoGBR_GRCh38, PyrhoGIH_GRCh38, PyrhoGWD_GRCh38, PyrhoIBS_GRCh38, PyrhoITU_GRCh38, PyrhoJPT_GRCh38, PyrhoKHV_GRCh38, PyrhoLWK_GRCh38, PyrhoMSL_GRCh38, PyrhoMXL_GRCh38, PyrhoPEL_GRCh38, PyrhoPJL_GRCh38, PyrhoPUR_GRCh38, PyrhoSTU_GRCh38, PyrhoTSI_GRCh38, PyrhoYRI_GRCh38
Specify a particular genetic map. By default, a chromosome-specific uniform recombination rate is used. These default rates are listed in the catalog: <https://popsim-consortium.github.io/stdpopsim-docs/stable/catalog.html> Available maps: HapMapII_GRCh37, HapMapII_GRCh38, DeCodeSexAveraged_GRCh36, DeCodeSexAveraged_GRCh38, PyrhoACB_GRCh38, PyrhoASW_GRCh38, PyrhoBEB_GRCh38, PyrhoCDX_GRCh38, PyrhoCEU_GRCh38, PyrhoCHB_GRCh38, PyrhoCHS_GRCh38, PyrhoCLM_GRCh38, PyrhoESN_GRCh38, PyrhoFIN_GRCh38, PyrhoGBR_GRCh38, PyrhoGIH_GRCh38, PyrhoGWD_GRCh38, PyrhoIBS_GRCh38, PyrhoITU_GRCh38, PyrhoJPT_GRCh38, PyrhoKHV_GRCh38, PyrhoLWK_GRCh38, PyrhoMSL_GRCh38, PyrhoMXL_GRCh38, PyrhoPEL_GRCh38, PyrhoPJL_GRCh38, PyrhoPUR_GRCh38, PyrhoSTU_GRCh38, PyrhoTSI_GRCh38, PyrhoYRI_GRCh38.
- --help-dfes
Print list of DFEs and exit. If a DFE ID is given as an argument, show help for this DFE. Otherwise show help for all available DFEs
- -c, --chromosome
Possible choices: 1, chr1, 2, chr2, 3, chr3, 4, chr4, 5, chr5, 6, chr6, 7, chr7, 8, chr8, 9, chr9, 10, chr10, 11, chr11, 12, chr12, 13, chr13, 14, chr14, 15, chr15, 16, chr16, 17, chr17, 18, chr18, 19, chr19, 20, chr20, 21, chr21, 22, chr22, X, chrX, Y, chrY, MT, chrM
Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y, MT. Default=None.
- -L, --length
Simulate a default contig of given length.
- -i, --inclusion-mask
Path to inclusion mask specified in bed format.
- -e, --exclusion-mask
Path to exclusion mask specified in bed format.
- -l, --length-multiplier
Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.
- --left
The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).
- --right
The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.
- -s, --seed
The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.
- --keep-mutation-ids-as-alleles
If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.
Default:
False- -d, --demographic-model
Possible choices: OutOfAfricaExtendedNeandertalAdmixturePulse_3I21, OutOfAfrica_3G09, OutOfAfrica_2T12, Africa_1T12, AmericanAdmixture_4B18, OutOfAfricaArchaicAdmixture_5R19, Zigzag_1S14, AncientEurasia_9K19, PapuansOutOfAfrica_10J19, AshkSub_7G19, OutOfAfrica_4J17, Africa_1B08, AncientEurope_4A21
Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: OutOfAfricaExtendedNeandertalAdmixturePulse_3I21, OutOfAfrica_3G09, OutOfAfrica_2T12, Africa_1T12, AmericanAdmixture_4B18, OutOfAfricaArchaicAdmixture_5R19, Zigzag_1S14, AncientEurasia_9K19, PapuansOutOfAfrica_10J19, AshkSub_7G19, OutOfAfrica_4J17, Africa_1B08, AncientEurope_4A21. Please see –help-models for details of these models.
- --dfe
Possible choices: Gamma_K17, Gamma_H17, LogNormal_H17, Mixed_K23, PosNeg_R24, GammaPos_Z21
Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:Gamma_K17, Gamma_H17, LogNormal_H17, Mixed_K23, PosNeg_R24, GammaPos_Z21. Please see –help-dfes for details of these DFE models.
- --dfe-interval
Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.
- --dfe-bed-file
A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.
- --help-annotations
Print list of annotations and exit. If a annotation ID is given as an argument, show help for this annotation. Otherwise show help for all available annotations
- --dfe-annotation
Possible choices: ensembl_havana_104_exons, ensembl_havana_104_CDS
Specify the intervals over which a given DFE acts using a genomic annotation track Available maps: ensembl_havana_104_exons, ensembl_havana_104_CDS.
- -o, --output
Where to write the output tree sequence file. Defaults to stdout if not specified
MusMus
Run simulations for Mus musculus using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘–output’ option to specify a filename.
Default population parameters for Mus musculus: Generation time: 0.75 Population size: 500000 Mutation rate: 5.4e-09 Recombination rate: 5.567e-09
stdpopsim MusMus [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
[--help-dfes [HELP_DFES]] [-c] [-L LENGTH]
[-i INCLUSION_MASK] [-e EXCLUSION_MASK]
[-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
[-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
[--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
samples [samples ...]
Positional Arguments
- samples
The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.
Named Arguments
- --help-models
Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models
- -b, --bibtex-file
Write citations to a given bib file. This will overwrite the file.
- -D, --dry-run
Do not run actual simulation
Default:
False- --help-dfes
Print list of DFEs and exit. If a DFE ID is given as an argument, show help for this DFE. Otherwise show help for all available DFEs
- -c, --chromosome
Possible choices: 1, chr1, 2, chr2, 3, chr3, 4, chr4, 5, chr5, 6, chr6, 7, chr7, 8, chr8, 9, chr9, 10, chr10, 11, chr11, 12, chr12, 13, chr13, 14, chr14, 15, chr15, 16, chr16, 17, chr17, 18, chr18, 19, chr19, X, chrX, Y, chrY, MT, chrM
Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, X, Y, MT. Default=None.
- -L, --length
Simulate a default contig of given length.
- -i, --inclusion-mask
Path to inclusion mask specified in bed format.
- -e, --exclusion-mask
Path to exclusion mask specified in bed format.
- -l, --length-multiplier
Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.
- --left
The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).
- --right
The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.
- -s, --seed
The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.
- --keep-mutation-ids-as-alleles
If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.
Default:
False- -d, --demographic-model
Possible choices: DomesticusEurope_1F22, MusculusKorea_1F22, CastaneusIndia_1F22
Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: DomesticusEurope_1F22, MusculusKorea_1F22, CastaneusIndia_1F22. Please see –help-models for details of these models.
- --dfe
Possible choices: Gamma_B21
Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:Gamma_B21. Please see –help-dfes for details of these DFE models.
- --dfe-interval
Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.
- --dfe-bed-file
A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.
- -o, --output
Where to write the output tree sequence file. Defaults to stdout if not specified
OrySat
Run simulations for Oryza sativa using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘–output’ option to specify a filename.
Default population parameters for Oryza sativa: Generation time: 1 Population size: 46875 Mutation rate: 3.2e-09 Recombination rate: 8.955e-10
stdpopsim OrySat [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D] [-c]
[-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
[-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
[-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
[--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
samples [samples ...]
Positional Arguments
- samples
The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.
Named Arguments
- --help-models
Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models
- -b, --bibtex-file
Write citations to a given bib file. This will overwrite the file.
- -D, --dry-run
Do not run actual simulation
Default:
False- -c, --chromosome
Possible choices: 1, chr1, Mt, Pt, 2, chr2, 3, chr3, 4, chr4, 5, chr5, 6, chr6, 7, chr7, 8, chr8, 9, chr9, 10, chr10, 11, chr11, 12, chr12
Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, Mt, Pt, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12. Default=None.
- -L, --length
Simulate a default contig of given length.
- -i, --inclusion-mask
Path to inclusion mask specified in bed format.
- -e, --exclusion-mask
Path to exclusion mask specified in bed format.
- -l, --length-multiplier
Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.
- --left
The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).
- --right
The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.
- -s, --seed
The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.
- --keep-mutation-ids-as-alleles
If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.
Default:
False- -d, --demographic-model
Possible choices: BottleneckMigration_3C07
Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: BottleneckMigration_3C07. Please see –help-models for details of these models.
- --dfe
Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.
- --dfe-interval
Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.
- --dfe-bed-file
A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.
- -o, --output
Where to write the output tree sequence file. Defaults to stdout if not specified
PanTro
Run simulations for Pan troglodytes using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.
Default population parameters for Pan troglodytes: Generation time: 24.6 Population size: 16781 Mutation rate: 1.6e-08 Recombination rate: 1.2e-08
stdpopsim PanTro [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D] [-c]
[-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
[-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
[-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
[--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
samples [samples ...]
Positional Arguments
- samples
The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.
Named Arguments
- --help-models
Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models
- -b, --bibtex-file
Write citations to a given bib file. This will overwrite the file.
- -D, --dry-run
Do not run actual simulation
Default:
False- -c, --chromosome
Possible choices: 1, chr1, 2A, chr2A, 2B, chr2B, 3, chr3, 4, chr4, 5, chr5, 6, chr6, 7, chr7, 8, chr8, 9, chr9, 10, chr10, 11, chr11, 12, chr12, 13, chr13, 14, chr14, 15, chr15, 16, chr16, 17, chr17, 18, chr18, 19, chr19, 20, chr20, 21, chr21, 22, chr22, X, chrX, Y, chrY
Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2A, 2B, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, Y. Default=None.
- -L, --length
Simulate a default contig of given length.
- -i, --inclusion-mask
Path to inclusion mask specified in bed format.
- -e, --exclusion-mask
Path to exclusion mask specified in bed format.
- -l, --length-multiplier
Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.
- --left
The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).
- --right
The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.
- -s, --seed
The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.
- --keep-mutation-ids-as-alleles
If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.
Default:
False- -d, --demographic-model
Possible choices: BonoboGhost_4K19
Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: BonoboGhost_4K19. Please see –help-models for details of these models.
- --dfe
Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.
- --dfe-interval
Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.
- --dfe-bed-file
A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.
- -o, --output
Where to write the output tree sequence file. Defaults to stdout if not specified
PapAnu
Run simulations for Papio anubis using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘–output’ option to specify a filename.
Default population parameters for Papio anubis: Generation time: 11 Population size: 335505 Mutation rate: 5.7e-09 Recombination rate: 1.124e-08
stdpopsim PapAnu [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE]
[--help-genetic-maps [HELP_GENETIC_MAPS]] [-D] [-g] [-c]
[-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
[-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
[-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
[--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
samples [samples ...]
Positional Arguments
- samples
The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.
Named Arguments
- --help-models
Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models
- -b, --bibtex-file
Write citations to a given bib file. This will overwrite the file.
- --help-genetic-maps
Print list of genetic maps and exit. If a genetic map ID is given as an argument, show help for this map. Otherwise show help for all available genetic maps
- -D, --dry-run
Do not run actual simulation
Default:
False- -g, --genetic-map
Possible choices: Pyrho_PAnubis1_0
Specify a particular genetic map. By default, a chromosome-specific uniform recombination rate is used. These default rates are listed in the catalog: <https://popsim-consortium.github.io/stdpopsim-docs/stable/catalog.html> Available maps: Pyrho_PAnubis1_0.
- -c, --chromosome
Possible choices: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, X, Y
Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, X, Y. Default=None.
- -L, --length
Simulate a default contig of given length.
- -i, --inclusion-mask
Path to inclusion mask specified in bed format.
- -e, --exclusion-mask
Path to exclusion mask specified in bed format.
- -l, --length-multiplier
Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.
- --left
The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).
- --right
The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.
- -s, --seed
The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.
- --keep-mutation-ids-as-alleles
If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.
Default:
False- -d, --demographic-model
Possible choices: SinglePopSMCpp_1W22
Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: SinglePopSMCpp_1W22. Please see –help-models for details of these models.
- --dfe
Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.
- --dfe-interval
Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.
- --dfe-bed-file
A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.
- -o, --output
Where to write the output tree sequence file. Defaults to stdout if not specified
PhoSin
Run simulations for Phocoena sinus using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.
Default population parameters for Phocoena sinus: Generation time: 11.9 Population size: 3500 Mutation rate: 5.83e-09 Recombination rate: 1e-08
stdpopsim PhoSin [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D]
[--help-dfes [HELP_DFES]] [-c] [-L LENGTH]
[-i INCLUSION_MASK] [-e EXCLUSION_MASK]
[-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
[-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
[--dfe-interval] [--dfe-bed-file]
[--help-annotations [HELP_ANNOTATIONS]] [--dfe-annotation]
[-o OUTPUT]
samples [samples ...]
Positional Arguments
- samples
The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.
Named Arguments
- --help-models
Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models
- -b, --bibtex-file
Write citations to a given bib file. This will overwrite the file.
- -D, --dry-run
Do not run actual simulation
Default:
False- --help-dfes
Print list of DFEs and exit. If a DFE ID is given as an argument, show help for this DFE. Otherwise show help for all available DFEs
- -c, --chromosome
Possible choices: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, X
Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, X. Default=None.
- -L, --length
Simulate a default contig of given length.
- -i, --inclusion-mask
Path to inclusion mask specified in bed format.
- -e, --exclusion-mask
Path to exclusion mask specified in bed format.
- -l, --length-multiplier
Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.
- --left
The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).
- --right
The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.
- -s, --seed
The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.
- --keep-mutation-ids-as-alleles
If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.
Default:
False- -d, --demographic-model
Possible choices: Vaquita2Epoch_1R22
Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: Vaquita2Epoch_1R22. Please see –help-models for details of these models.
- --dfe
Possible choices: Gamma_R22
Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:Gamma_R22. Please see –help-dfes for details of these DFE models.
- --dfe-interval
Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.
- --dfe-bed-file
A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.
- --help-annotations
Print list of annotations and exit. If a annotation ID is given as an argument, show help for this annotation. Otherwise show help for all available annotations
- --dfe-annotation
Possible choices: Phocoena_sinus.mPhoSin1.pri.110_exons, Phocoena_sinus.mPhoSin1.pri.110_CDS
Specify the intervals over which a given DFE acts using a genomic annotation track Available maps: Phocoena_sinus.mPhoSin1.pri.110_exons, Phocoena_sinus.mPhoSin1.pri.110_CDS.
- -o, --output
Where to write the output tree sequence file. Defaults to stdout if not specified
PonAbe
Run simulations for Pongo abelii using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘–output’ option to specify a filename.
Default population parameters for Pongo abelii: Generation time: 25 Population size: 17900.0 Mutation rate: 1.5e-08 Recombination rate: 6.403e-09
stdpopsim PonAbe [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE]
[--help-genetic-maps [HELP_GENETIC_MAPS]] [-D] [-g] [-c]
[-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
[-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
[-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
[--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
samples [samples ...]
Positional Arguments
- samples
The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.
Named Arguments
- --help-models
Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models
- -b, --bibtex-file
Write citations to a given bib file. This will overwrite the file.
- --help-genetic-maps
Print list of genetic maps and exit. If a genetic map ID is given as an argument, show help for this map. Otherwise show help for all available genetic maps
- -D, --dry-run
Do not run actual simulation
Default:
False- -g, --genetic-map
Possible choices: NaterPA_PonAbe3, NaterPP_PonAbe3
Specify a particular genetic map. By default, a chromosome-specific uniform recombination rate is used. These default rates are listed in the catalog: <https://popsim-consortium.github.io/stdpopsim-docs/stable/catalog.html> Available maps: NaterPA_PonAbe3, NaterPP_PonAbe3.
- -c, --chromosome
Possible choices: 1, chr1, 2A, 2a, chr2a, chr2A, 2B, 2b, chr2b, chr2B, 3, chr3, 4, chr4, 5, chr5, 6, chr6, 7, chr7, 8, chr8, 9, chr9, 10, chr10, 11, chr11, 12, chr12, 13, chr13, 14, chr14, 15, chr15, 16, chr16, 17, chr17, 18, chr18, 19, chr19, 20, chr20, 21, chr21, 22, chr22, X, chrX, MT, chrM
Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2A, 2B, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, X, MT. Default=None.
- -L, --length
Simulate a default contig of given length.
- -i, --inclusion-mask
Path to inclusion mask specified in bed format.
- -e, --exclusion-mask
Path to exclusion mask specified in bed format.
- -l, --length-multiplier
Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.
- --left
The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).
- --right
The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.
- -s, --seed
The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.
- --keep-mutation-ids-as-alleles
If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.
Default:
False- -d, --demographic-model
Possible choices: TwoSpecies_2L11
Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: TwoSpecies_2L11. Please see –help-models for details of these models.
- --dfe
Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.
- --dfe-interval
Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.
- --dfe-bed-file
A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.
- -o, --output
Where to write the output tree sequence file. Defaults to stdout if not specified
RatNor
Run simulations for Rattus norvegicus using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.
Default population parameters for Rattus norvegicus: Generation time: 0.5 Population size: 124000.0 Mutation rate: 2.96e-09 Recombination rate: 6.103e-09
stdpopsim RatNor [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D] [-c]
[-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
[-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
[-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
[--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
samples [samples ...]
Positional Arguments
- samples
The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.
Named Arguments
- --help-models
Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models
- -b, --bibtex-file
Write citations to a given bib file. This will overwrite the file.
- -D, --dry-run
Do not run actual simulation
Default:
False- -c, --chromosome
Possible choices: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, X, Y, MT
Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, X, Y, MT. Default=None.
- -L, --length
Simulate a default contig of given length.
- -i, --inclusion-mask
Path to inclusion mask specified in bed format.
- -e, --exclusion-mask
Path to exclusion mask specified in bed format.
- -l, --length-multiplier
Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.
- --left
The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).
- --right
The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.
- -s, --seed
The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.
- --keep-mutation-ids-as-alleles
If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.
Default:
False- -d, --demographic-model
Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: . Please see –help-models for details of these models.
- --dfe
Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.
- --dfe-interval
Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.
- --dfe-bed-file
A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.
- -o, --output
Where to write the output tree sequence file. Defaults to stdout if not specified
StrAga
Run simulations for Streptococcus agalactiae using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘– output’ option to specify a filename.
Default population parameters for Streptococcus agalactiae: Generation time: 0.0027397260273972603 Population size: 140000 Mutation rate: 1.53e-09 Recombination rate: 1.53e-10 Bacterial recombination with tract length: 120000
stdpopsim StrAga [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D] [-c]
[-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
[-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
[-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
[--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
samples [samples ...]
Positional Arguments
- samples
The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.
Named Arguments
- --help-models
Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models
- -b, --bibtex-file
Write citations to a given bib file. This will overwrite the file.
- -D, --dry-run
Do not run actual simulation
Default:
False- -c, --chromosome
Possible choices: 1, I, chr1
Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1. Default=None.
- -L, --length
Simulate a default contig of given length.
- -i, --inclusion-mask
Path to inclusion mask specified in bed format.
- -e, --exclusion-mask
Path to exclusion mask specified in bed format.
- -l, --length-multiplier
Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.
- --left
The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).
- --right
The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.
- -s, --seed
The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.
- --keep-mutation-ids-as-alleles
If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.
Default:
False- -d, --demographic-model
Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: . Please see –help-models for details of these models.
- --dfe
Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.
- --dfe-interval
Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.
- --dfe-bed-file
A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.
- -o, --output
Where to write the output tree sequence file. Defaults to stdout if not specified
SusScr
Run simulations for Sus scrofa using up-to-date genome information, genetic maps and simulation models from the literature. NOTE: By default, the tskit ‘.trees’ binary file is written to stdout,so you should either redirect this to a file or use the ‘–output’ option to specify a filename.
Default population parameters for Sus scrofa: Generation time: 3.6 Population size: 270000 Mutation rate: 3.6e-09 Recombination rate: 9.248e-09
stdpopsim SusScr [-h] [--help-models [HELP_MODELS]] [-b BIBTEX_FILE] [-D] [-c]
[-L LENGTH] [-i INCLUSION_MASK] [-e EXCLUSION_MASK]
[-l LENGTH_MULTIPLIER] [--left LEFT] [--right RIGHT]
[-s SEED] [--keep-mutation-ids-as-alleles] [-d] [--dfe]
[--dfe-interval] [--dfe-bed-file] [-o OUTPUT]
samples [samples ...]
Positional Arguments
- samples
The number of samples to draw from each population. At least two genomes must be sampled, say, for one diploid individual. The number of arguments accepted depends on the specified simulation model: for a model that has n populations, we can specify the number of samples to draw from each of these populations.We do not need to provide sample numbers of each of the populations; those that are omitted are set to zero.
Named Arguments
- --help-models
Print descriptions of simulation models and exit. If a model ID is provided as an argument show help for this model; otherwise show help for all available models
- -b, --bibtex-file
Write citations to a given bib file. This will overwrite the file.
- -D, --dry-run
Do not run actual simulation
Default:
False- -c, --chromosome
Possible choices: 1, chr1, 2, chr2, 3, chr3, 4, chr4, 5, chr5, 6, chr6, 7, chr7, 8, chr8, 9, chr9, 10, chr10, 11, chr11, 12, chr12, 13, chr13, 14, chr14, 15, chr15, 16, chr16, 17, chr17, 18, chr18, X, chrX, Y, chrY, MT
Simulate a specific chromosome. If no chromosome is given, simulate a generic contig of given length, specified using –length. Options: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, X, Y, MT. Default=None.
- -L, --length
Simulate a default contig of given length.
- -i, --inclusion-mask
Path to inclusion mask specified in bed format.
- -e, --exclusion-mask
Path to exclusion mask specified in bed format.
- -l, --length-multiplier
Deprecated: use left/right instead. Simulate a sequence of length l times the named chromosome’s length using the named chromosome’s mutation and recombination rates.
- --left
The leftmost coordinate (inclusive) of the contig on the named chromosome. Defaults to 0 (the beginning of the chromosome).
- --right
The rightmost coordinate (exclusive) of the contig on the named chromosome. Defaults to the length of the chromosome.
- -s, --seed
The random seed to use for simulations. If not specified a high-quality random seed will be generated automatically. For msprime, seeds must be > 0 and < 2^32.
- --keep-mutation-ids-as-alleles
If set, mutations in SLiM simulations will have alleles coded as numeric ids rather than random nucleotides.
Default:
False- -d, --demographic-model
Specify a simulation model. If no model is specified, a single population constant size model is used. Available models: . Please see –help-models for details of these models.
- --dfe
Specify a Distribution of Fitness Effects (DFE) model. If no DFE is specified, all mutations are neutral. Available DFE models:. Please see –help-dfes for details of these DFE models.
- --dfe-interval
Specify the interval where selection (given a DFE) is simulated. Anything outside of the interval is simulated as neutral. If no interval is specified, selection is simulated across the entire contig. The interval is written as ‘start,end’ (separated by a comma, with no space, for instance: –dfe-interval 1000,2000.
- --dfe-bed-file
A bed file specifing the intervals where selection (given a DFE) is simulated. Non-overlapping intervals belonging to the same chromosome are required. If no interval is specified, selection is simulated across the entire contig. See also –dfe-interval and –dfe-annotation.
- -o, --output
Where to write the output tree sequence file. Defaults to stdout if not specified
download-genetic-maps
Download genetic maps and store them in the cache directory. Maps are downloaded regardless of whether they are already in the cache or not. Please use the –cache-dir option to download maps to a specific directory.
stdpopsim download-genetic-maps [-h] [species] [genetic_maps ...]
Positional Arguments
- species
Download genetic maps for this species. If not specified download all known genetic maps.
- genetic_maps
If specified, download these genetic maps. If no maps are provided, download all maps for this species.