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cli-call-help.txt
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cli-call-help.txt
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usage: MCMC haplotype calling [-h] [--haplotypes HAPLOTYPES]
[--prior-frequencies PRIOR_FREQUENCIES]
[--filter-input-haplotypes FILTER_INPUT_HAPLOTYPES]
[--bam BAM [BAM ...]] [--ploidy PLOIDY]
[--inbreeding INBREEDING]
[--sample-pool SAMPLE_POOL]
[--reference REFERENCE]
[--base-error-rate BASE_ERROR_RATE]
[--use-base-phred-scores]
[--mapping-quality MAPPING_QUALITY]
[--keep-duplicate-reads] [--keep-qcfail-reads]
[--keep-supplementary-reads]
[--read-group-field READ_GROUP_FIELD]
[--report [REPORT ...]] [--cores CORES]
[--mcmc-chains MCMC_CHAINS]
[--mcmc-steps MCMC_STEPS]
[--mcmc-burn MCMC_BURN] [--mcmc-seed MCMC_SEED]
[--mcmc-chain-incongruence-threshold MCMC_CHAIN_INCONGRUENCE_THRESHOLD]
options:
-h, --help show this help message and exit
--haplotypes HAPLOTYPES
Tabix indexed VCF file containing haplotype/MNP/SNP
variants to be re-called among input samples.
--prior-frequencies PRIOR_FREQUENCIES
Optionally specify an INFO field within the input VCF
file to designate as prior allele frequencies for the
input haplotypes. This can be any numerical field of
length 'R' and these values will automatically be
normalized.
--filter-input-haplotypes FILTER_INPUT_HAPLOTYPES
Optionally filter input haplotypes using a string of
the form '<field><operator><value>' where <field> is a
numerical INFO field with length 'A' or 'R',
<operator> is one of =|>|<|>=|<=|!=, and <value> is a
numerical value.
--bam BAM [BAM ...] Bam file(s) to use in analysis. This may be (1) a list
of one or more bam filepaths, (2) a plain-text file
containing a single bam filepath on each line, (3) a
plain-text file containing a sample identifier and its
corresponding bam filepath on each line separated by a
tab. If options (1) or (2) are used then all samples
within each bam will be used within the analysis. If
option (3) is used then only the specified sample will
be extracted from each bam file and An error will be
raised if a sample is not found within its specified
bam file.
--ploidy PLOIDY Specify sample ploidy (default = 2).This may be (1) a
single integer used to specify the ploidy of all
samples or (2) a file containing a list of all samples
and their ploidy. If option (2) is used then each line
of the plaintext file must contain a single sample
identifier and the ploidy of that sample separated by
a tab.
--inbreeding INBREEDING
Specify expected sample inbreeding coefficient
(default = 0.0).This may be (1) a single floating
point value in the interval [0, 1] used to specify the
inbreeding coefficient of all samples or (2) a file
containing a list of all samples and their inbreeding
coefficient. If option (2) is used then each line of
the plaintext file must contain a single sample
identifier and the inbreeding coefficient of that
sample separated by a tab.
--sample-pool SAMPLE_POOL
WARNING: this is an experimental feature!!! Pool
samples together into a single genotype. This may be
(1) the name of a single pool for all samples or (2) a
file containing a list of all samples and their
assigned pool. If option (2) is used then each line of
the plaintext file must contain a single sample
identifier and the name of a pool separated by a
tab.Samples may be assigned to multiple pools by using
the same sample name on multiple lines.Each pool will
treated as a single genotype by combining all reads
from its constituent samples. Note that the pool names
should be used in place of the samples names when
assigning other per-sample parameters such as ploidy
or inbreeding coefficients.
--reference REFERENCE
Indexed fasta file containing the reference genome.
--base-error-rate BASE_ERROR_RATE
Expected base error rate of read sequences (default =
0.0024). The default value comes from Pfeiffer et al
2018 and is a general estimate for Illumina short
reads.
--use-base-phred-scores
Flag: use base phred-scores as a source of base error
rate. This will use the phred-encoded per base scores
in addition to the general error rate specified by the
--base-error-rate argument. Using this option can slow
down assembly speed.
--mapping-quality MAPPING_QUALITY
Minimum mapping quality of reads used in assembly
(default = 20).
--keep-duplicate-reads
Flag: Use reads marked as duplicates in the assembly
(these are skipped by default).
--keep-qcfail-reads Flag: Use reads marked as qcfail in the assembly
(these are skipped by default).
--keep-supplementary-reads
Flag: Use reads marked as supplementary in the
assembly (these are skipped by default).
--read-group-field READ_GROUP_FIELD
Read group field to use as sample id (default = "SM").
The chosen field determines tha sample ids required in
other input files e.g. the --sample-list argument.
--report [REPORT ...]
Extra fields to report within the output VCF: AFPRIOR
= prior allele frequencies; AFP = posterior mean
allele frequencies; AOP = posterior probability of
allele occurring at any copy number; GP = genotype
posterior probabilities; GL = genotype likelihoods.
--cores CORES Number of cpu cores to use (default = 1).
--mcmc-chains MCMC_CHAINS
Number of independent MCMC chains per assembly
(default = 2).
--mcmc-steps MCMC_STEPS
Number of steps to simulate in each MCMC chain
(default = 2000).
--mcmc-burn MCMC_BURN
Number of initial steps to discard from each MCMC
chain (default = 1000).
--mcmc-seed MCMC_SEED
Random seed for MCMC (default = 42).
--mcmc-chain-incongruence-threshold MCMC_CHAIN_INCONGRUENCE_THRESHOLD
Posterior phenotype probability threshold for
identification of incongruent posterior modes (default
= 0.60).