genetic_demux/freebayes

Description

Freebayes is a Bayesian genetic variant detector designed to
find small polymorphisms, specifically SNPs.

Type

bash_script

License

MIT

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
pvar: [ 0 ]  
theta: [ 0.001 ]  
ploidy: [ 2 ]  
reference_quality: [ "100,60" ]  
use_best_n_alleles: [ 0 ]  
max_complex_gap: [ 3 ]  
min_repeat_size: [ 5 ]  
min_repeat_entropy: [ 1 ]  
min_mapping_quality: [ 1 ]  
min_base_quality: [ 1 ]  
min_supporting_allele_qsum: [ 0 ]  
min_supporting_mapping_qsum: [ 0 ]  
mismatch_base_quality_threshold: [ 10 ]  
read_max_mismatch_fraction: [ 1 ]  
min_alternate_fraction: [ 0.05 ]  
min_alternate_count: [ 2 ]  
min_alternate_qsum: [ 0 ]  
min_alternate_total: [ 1 ]  
min_coverage: [ 0 ]  
prob_contamination: [ 1e-8 ]  
genotyping_max_iterations: [ 1000 ]  
genotyping_max_banddepth: [ 6 ]  
posterior_integration_limits: [ "1,3" ]  
read_dependence_factor: [ 0.9 ]  
output: "$id.$key.output.freebayes_out"  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v3.0.0 \  
  -main-script target/nextflow/genetic_demux/freebayes/main.nf \  
  -params-file params.yaml

Input

Name	Type & Properties	Description
--bam	file	Add FILE to the set of BAM files to be analyzed.
--bam_list	file	A file containing a list of BAM files to be analyzed.
--stdin	boolean_true	Read BAM input on stdin.
--fasta_reference	file	Use FILE as the reference sequence for analysis. An index file (FILE.fai) will be created if none exists. If neither --targets nor --region are specified, FreeBayes will analyze every position in this reference.
--fasta_reference_index	file	Use FILE.fai as the index of reference sequence for analysis.
--targets	file	Limit analysis to targets listed in the BED-format FILE.
--region	string	Limit analysis to the specified region, 0-base coordinates, end_position not included (same as BED format).
--samples	file	Limit analysis to samples listed (one per line) in the FILE. By default FreeBayes will analyze all samples in its input BAM files.
--populations	file	Each line of FILE should list a sample and a population which it is part of. The population-based bayesian inference model will then be partitioned on the basis of the populations.
--cnv_map	file	Read a copy number map from the BED file FILE, which has either a sample-level ploidy or a region-specific format.
--gvcf	boolean_true	Write gVCF output, which indicates coverage in uncalled regions.
--gvcf_chunk	integer	When writing gVCF output emit a record for every NUM bases.
--variant_input	file	Use variants reported in VCF file as input to the algorithm. Variants in this file will included in the output even if there is not enough support in the data to pass input filters.
--only_use_input_alleles	boolean_true	Only provide variant calls and genotype likelihoods for sites and alleles which are provided in the VCF input, and provide output in the VCF for all input alleles, not just those which have support in the data.
--haplotype_basis_alleles	file	When specified, only variant alleles provided in this input VCF will be used for the construction of complex or haplotype alleles.
--report_all_haplotype_alleles	boolean_true	At sites where genotypes are made over haplotype alleles, provide information about all alleles in output, not only those which are called.
--report_monomorphic	boolean_true	Report even loci which appear to be monomorphic, and report all considered alleles, even those which are not in called genotypes.
--pvar	double	Report sites if the probability that there is a polymorphism at the site is greater than N. Note that post-filtering is generally recommended over the use of this parameter.
--strict_vcf	boolean_true	Generate strict VCF format (FORMAT/GQ will be an int).
--theta	double	The expected mutation rate or pairwise nucleotide diversity among the population under analysis. This serves as the single parameter to the Ewens Sampling Formula prior model.
--ploidy	integer	Sets the default ploidy for the analysis to N.
--pooled_discrete	boolean_true	Assume that samples result from pooled sequencing. Model pooled samples using discrete genotypes across pools.
--pooled_continuous	boolean_true	Output all alleles which pass input filters, regardles of genotyping outcome or model.
--use_reference_allele	boolean_true	This flag includes the reference allele in the analysis as if it is another sample from the same population.
--reference_quality	string	Assign mapping quality of MQ to the reference allele at each site and base quality of BQ.
--throw_away_snp_obs	boolean_true	Ignore SNP alleles.
--throw_away_mnps_obs	boolean_false	Ignore multi-nuceotide polymorphisms, MNPs. MNPs are excluded as default.
--throw_away_indel_obs	boolean_false	Ignore insertion and deletion alleles. Indels are excluded as default.
--throw_away_complex_obs	boolean_false	Ignore complex events (composites of other classes). Complex are excluded as default
--use_best_n_alleles	integer	Evaluate only the best N SNP alleles, ranked by sum of supporting quality scores.
--max_complex_gap	integer	Allow haplotype calls with contiguous embedded matches of up to this length.
--min_repeat_size	integer	When assembling observations across repeats, require the total repeat length at least this many bp.
--min_repeat_entropy	integer	To detect interrupted repeats, build across sequence until it has entropy > N bits per bp. Set to 0 to turn off.
--no_partial_observations	boolean_true	Exclude observations which do not fully span the dynamically-determined detection window. (default, use all observations, dividing partial support across matching haplotypes when generating haplotypes.)
--dont_left_align_indels	boolean_true	Turn off left-alignment of indels, which is enabled by default.
--use_duplicate_reads	boolean_true	Include duplicate-marked alignments in the analysis. default: exclude duplicates marked as such in alignments
--min_mapping_quality	integer	Exclude alignments from analysis if they have a mapping quality less than Q.
--min_base_quality	integer	Exclude alleles from analysis if their supporting base quality is less than Q. Default value is changed according to the instruction of scSplit.
--min_supporting_allele_qsum	integer	Consider any allele in which the sum of qualities of supporting observations is at least Q.
--min_supporting_mapping_qsum	integer	Consider any allele in which and the sum of mapping qualities of supporting reads is at least.
--mismatch_base_quality_threshold	integer	Count mismatches toward --read-mismatch-limit if the base quality of the mismatch is >= Q.
--read_max_mismatch_fraction	double	Exclude reads with more than N mismatches where each mismatch has base quality >= mismatch-base-quality-threshold.
--read_mismatch_limit	integer	Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= mismatch-base-quality-threshold.
--read_snp_limit	integer	Exclude reads with more than N base mismatches, ignoring gaps with quality >= mismatch-base-quality-threshold.
--read_indel_limit	integer	Exclude reads with more than N separate gaps.
--standard_filters	boolean_true	Use stringent input base and mapping quality filters, equivalent to -m 30 -q 20 -R 0 -S 0
--min_alternate_fraction	double	Require at least this fraction of observations supporting an alternate allele within a single individual in order to evaluate the position.
--min_alternate_count	integer	Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position.
--min_alternate_qsum	integer	Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position.
--min_alternate_total	integer	Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis.
--min_coverage	integer	Require at least this coverage to process a site.
--max_coverage	integer	Do not process sites with greater than this coverage.
--no_population_priors	boolean_true	Equivalent to --pooled-discrete --hwe-priors-off and removal of Ewens Sampling Formula component of priors.
--hwe_priors_off	boolean_true	Disable estimation of the probability of the combination arising under HWE given the allele frequency as estimated by observation frequency.
--binomial_obs_priors_off	boolean_true	Disable incorporation of prior expectations about observations. Uses read placement probability, strand balance probability, and read position probability.
--allele_balance_priors_off	boolean_true	Disable use of aggregate probability of observation balance between alleles as a component of the priors.
--observation_bias	file	Read length-dependent allele observation biases from FILE. The format is [length] [alignment efficiency relative to reference] where the efficiency is 1 if there is no relative observation bias.
--base_quality_cap	integer	Limit estimated observation quality by capping base quality at Q.
--prob_contamination	double	An estimate of contamination to use for all samples.
--legacy_gls	boolean_true	Use legacy (polybayes equivalent) genotype likelihood calculations
--contamination_estimates	file	A file containing per-sample estimates of contamination, such as those generated by VerifyBamID.
--report_genotype_likelihood_max	boolean_true	Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods.
--genotyping_max_iterations	integer	Iterate no more than N times during genotyping step.
--genotyping_max_banddepth	integer	Integrate no deeper than the Nth best genotype by likelihood when genotyping.
--posterior_integration_limits	string	Integrate all genotype combinations in our posterior space which include no more than N samples with their Mth best data likelihood.
--exclude_unobserved_genotypes	boolean_true	Skip sample genotypings for which the sample has no supporting reads.
--genotype_variant_threshold	integer	Limit posterior integration to samples where the second-best genotype likelihood is no more than log(N) from the highest genotype likelihood for the sample.
--use_mapping_quality	boolean_true	Use mapping quality of alleles when calculating data likelihoods.
--harmonic_indel_quality	boolean_true	Use a weighted sum of base qualities around an indel, scaled by the distance from the indel. By default use a minimum BQ in flanking sequence.
--read_dependence_factor	double	Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations.
--genotype_qualities	boolean_true	Calculate the marginal probability of genotypes and report as GQ in each sample field in the VCF output.
--debug	boolean_true	Print debugging output.
--dd	boolean_true	Print more verbose debugging output

Name

Type & Properties

--bam

file

--bam_list

file

--stdin

boolean_true

--fasta_reference

file

--fasta_reference_index

file

--targets

file

--region

string

--samples

file

--populations

file

--cnv_map

file

--gvcf

boolean_true

--gvcf_chunk

integer

--variant_input

file

--only_use_input_alleles

boolean_true

--haplotype_basis_alleles

file

--report_all_haplotype_alleles

boolean_true

--report_monomorphic

boolean_true

--pvar

double

--strict_vcf

boolean_true

--theta

double

--ploidy

integer

--pooled_discrete

boolean_true

--pooled_continuous

boolean_true

--use_reference_allele

boolean_true

--reference_quality

string

--throw_away_snp_obs

boolean_true

--throw_away_mnps_obs

boolean_false

--throw_away_indel_obs

boolean_false

--throw_away_complex_obs

boolean_false

--use_best_n_alleles

integer

--max_complex_gap

integer

--min_repeat_size

integer

--min_repeat_entropy

integer

--no_partial_observations

boolean_true

--dont_left_align_indels

boolean_true

--use_duplicate_reads

boolean_true

--min_mapping_quality

integer

--min_base_quality

integer

--min_supporting_allele_qsum

integer

--min_supporting_mapping_qsum

integer

--mismatch_base_quality_threshold

integer

--read_max_mismatch_fraction

double

--read_mismatch_limit

integer

--read_snp_limit

integer

--read_indel_limit

integer

--standard_filters

boolean_true

--min_alternate_fraction

double

--min_alternate_count

integer

--min_alternate_qsum

integer

--min_alternate_total

integer

--min_coverage

integer

--max_coverage

integer

--no_population_priors

boolean_true

--hwe_priors_off

boolean_true

--binomial_obs_priors_off

boolean_true

--allele_balance_priors_off

boolean_true

--observation_bias

file

--base_quality_cap

integer

--prob_contamination

double

--legacy_gls

boolean_true

--contamination_estimates

file

--report_genotype_likelihood_max

boolean_true

--genotyping_max_iterations

integer

--genotyping_max_banddepth

integer

--posterior_integration_limits

string

--exclude_unobserved_genotypes

boolean_true

--genotype_variant_threshold

integer

--use_mapping_quality

boolean_true

--harmonic_indel_quality

boolean_true

--read_dependence_factor

double

--genotype_qualities

boolean_true

--debug

boolean_true

--dd

boolean_true

Output

Name	Type & Properties	Description
--output -o	file output	Output directory
--vcf	string	Output VCF-format results to FILE.

Name

Type & Properties

--output

-o

file

output

--vcf

string