Freebayes

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

Info

ID: freebayes
Namespace: genetic_demux

Example commands

You can run the pipeline using nextflow run.

View help

You can use --help as a parameter to get an overview of the possible parameters.

nextflow run openpipelines-bio/openpipeline \
  -r 1.0.2 -latest \
  -main-script target/nextflow/genetic_demux/freebayes/main.nf \
  --help

Run command

Example of params.yaml 
# Input
# bam: "path/to/file"
# bam_list: "path/to/file"
stdin: false
# fasta_reference: "path/to/file"
# fasta_reference_index: "path/to/file"
# targets: "path/to/file"
# region: "foo"
# samples: "path/to/file"
# populations: "path/to/file"
# cnv_map: "path/to/file"
gvcf: false
# gvcf_chunk: 123
# variant_input: "path/to/file"
only_use_input_alleles: false
# haplotype_basis_alleles: "path/to/file"
report_all_haplotype_alleles: false
report_monomorphic: false
pvar: 0.0
strict_vcf: false
theta: 0.001
ploidy: 2
pooled_discrete: false
pooled_continuous: false
use_reference_allele: false
reference_quality: "100,60"
throw_away_snp_obs: false
throw_away_mnps_obs: true
throw_away_indel_obs: true
throw_away_complex_obs: true
use_best_n_alleles: 0
max_complex_gap: 3
min_repeat_size: 5
min_repeat_entropy: 1
no_partial_observations: false
dont_left_align_indels: false
use_duplicate_reads: false
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: 1.0
# read_mismatch_limit: 123
# read_snp_limit: 123
# read_indel_limit: 123
standard_filters: false
min_alternate_fraction: 0.05
min_alternate_count: 2
min_alternate_qsum: 0
min_alternate_total: 1
min_coverage: 0
# max_coverage: 123
no_population_priors: false
hwe_priors_off: false
binomial_obs_priors_off: false
allele_balance_priors_off: false
# observation_bias: "path/to/file"
# base_quality_cap: 123
prob_contamination: 1.0E-8
legacy_gls: false
# contamination_estimates: "path/to/file"
report_genotype_likelihood_max: false
genotyping_max_iterations: 1000
genotyping_max_banddepth: 6
posterior_integration_limits: "1,3"
exclude_unobserved_genotypes: false
# genotype_variant_threshold: 123
use_mapping_quality: false
harmonic_indel_quality: false
read_dependence_factor: 0.9
genotype_qualities: false
debug: false
dd: false

# Output
# output: "$id.$key.output.output"
# vcf: "snp.vcf"

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"
nextflow run openpipelines-bio/openpipeline \
  -r 1.0.2 -latest \
  -profile docker \
  -main-script target/nextflow/genetic_demux/freebayes/main.nf \
  -params-file params.yaml
Note

Replace -profile docker with -profile podman or -profile singularity depending on the desired backend.

Argument groups

Input

Name Description Attributes
--bam Add FILE to the set of BAM files to be analyzed. file
--bam_list A file containing a list of BAM files to be analyzed. file
--stdin Read BAM input on stdin. boolean_true
--fasta_reference 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. file
--fasta_reference_index Use FILE.fai as the index of reference sequence for analysis. file
--targets Limit analysis to targets listed in the BED-format FILE. file
--region Limit analysis to the specified region, 0-base coordinates, end_position not included (same as BED format). string
--samples Limit analysis to samples listed (one per line) in the FILE. By default FreeBayes will analyze all samples in its input BAM files. file
--populations 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. file
--cnv_map Read a copy number map from the BED file FILE, which has either a sample-level ploidy or a region-specific format. file
--gvcf Write gVCF output, which indicates coverage in uncalled regions. boolean_true
--gvcf_chunk When writing gVCF output emit a record for every NUM bases. integer
--variant_input 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. file
--only_use_input_alleles 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. boolean_true
--haplotype_basis_alleles When specified, only variant alleles provided in this input VCF will be used for the construction of complex or haplotype alleles. file
--report_all_haplotype_alleles At sites where genotypes are made over haplotype alleles, provide information about all alleles in output, not only those which are called. boolean_true
--report_monomorphic Report even loci which appear to be monomorphic, and report all considered alleles, even those which are not in called genotypes. boolean_true
--pvar 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. double, default: 0
--strict_vcf Generate strict VCF format (FORMAT/GQ will be an int). boolean_true
--theta 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. double, default: 0.001
--ploidy Sets the default ploidy for the analysis to N. integer, default: 2
--pooled_discrete Assume that samples result from pooled sequencing. Model pooled samples using discrete genotypes across pools. boolean_true
--pooled_continuous Output all alleles which pass input filters, regardles of genotyping outcome or model. boolean_true
--use_reference_allele This flag includes the reference allele in the analysis as if it is another sample from the same population. boolean_true
--reference_quality Assign mapping quality of MQ to the reference allele at each site and base quality of BQ. string, default: "100,60"
--throw_away_snp_obs Ignore SNP alleles. boolean_true
--throw_away_mnps_obs Ignore multi-nuceotide polymorphisms, MNPs. MNPs are excluded as default. boolean_false
--throw_away_indel_obs Ignore insertion and deletion alleles. Indels are excluded as default. boolean_false
--throw_away_complex_obs Ignore complex events (composites of other classes). Complex are excluded as default boolean_false
--use_best_n_alleles Evaluate only the best N SNP alleles, ranked by sum of supporting quality scores. integer, default: 0
--max_complex_gap Allow haplotype calls with contiguous embedded matches of up to this length. integer, default: 3
--min_repeat_size When assembling observations across repeats, require the total repeat length at least this many bp. integer, default: 5
--min_repeat_entropy To detect interrupted repeats, build across sequence until it has entropy > N bits per bp. Set to 0 to turn off. integer, default: 1
--no_partial_observations 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.) boolean_true
--dont_left_align_indels Turn off left-alignment of indels, which is enabled by default. boolean_true
--use_duplicate_reads Include duplicate-marked alignments in the analysis. default: exclude duplicates marked as such in alignments boolean_true
--min_mapping_quality Exclude alignments from analysis if they have a mapping quality less than Q. integer, default: 1
--min_base_quality Exclude alleles from analysis if their supporting base quality is less than Q. Default value is changed according to the instruction of scSplit. integer, default: 1
--min_supporting_allele_qsum Consider any allele in which the sum of qualities of supporting observations is at least Q. integer, default: 0
--min_supporting_mapping_qsum Consider any allele in which and the sum of mapping qualities of supporting reads is at least. integer, default: 0
--mismatch_base_quality_threshold Count mismatches toward –read-mismatch-limit if the base quality of the mismatch is >= Q. integer, default: 10
--read_max_mismatch_fraction Exclude reads with more than N mismatches where each mismatch has base quality >= mismatch-base-quality-threshold. double, default: 1
--read_mismatch_limit Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= mismatch-base-quality-threshold. integer
--read_snp_limit Exclude reads with more than N base mismatches, ignoring gaps with quality >= mismatch-base-quality-threshold. integer
--read_indel_limit Exclude reads with more than N separate gaps. integer
--standard_filters Use stringent input base and mapping quality filters, equivalent to -m 30 -q 20 -R 0 -S 0 boolean_true
--min_alternate_fraction Require at least this fraction of observations supporting an alternate allele within a single individual in order to evaluate the position. double, default: 0.05
--min_alternate_count Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position. integer, default: 2
--min_alternate_qsum Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position. integer, default: 0
--min_alternate_total Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis. integer, default: 1
--min_coverage Require at least this coverage to process a site. integer, default: 0
--max_coverage Do not process sites with greater than this coverage. integer
--no_population_priors Equivalent to –pooled-discrete –hwe-priors-off and removal of Ewens Sampling Formula component of priors. boolean_true
--hwe_priors_off Disable estimation of the probability of the combination arising under HWE given the allele frequency as estimated by observation frequency. boolean_true
--binomial_obs_priors_off Disable incorporation of prior expectations about observations. Uses read placement probability, strand balance probability, and read position probability. boolean_true
--allele_balance_priors_off Disable use of aggregate probability of observation balance between alleles as a component of the priors. boolean_true
--observation_bias 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. file
--base_quality_cap Limit estimated observation quality by capping base quality at Q. integer
--prob_contamination An estimate of contamination to use for all samples. double, default: 1e-08
--legacy_gls Use legacy (polybayes equivalent) genotype likelihood calculations boolean_true
--contamination_estimates A file containing per-sample estimates of contamination, such as those generated by VerifyBamID. file
--report_genotype_likelihood_max Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods. boolean_true
--genotyping_max_iterations Iterate no more than N times during genotyping step. integer, default: 1000
--genotyping_max_banddepth Integrate no deeper than the Nth best genotype by likelihood when genotyping. integer, default: 6
--posterior_integration_limits Integrate all genotype combinations in our posterior space which include no more than N samples with their Mth best data likelihood. string, default: "1,3"
--exclude_unobserved_genotypes Skip sample genotypings for which the sample has no supporting reads. boolean_true
--genotype_variant_threshold 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. integer
--use_mapping_quality Use mapping quality of alleles when calculating data likelihoods. boolean_true
--harmonic_indel_quality 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. boolean_true
--read_dependence_factor Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations. double, default: 0.9
--genotype_qualities Calculate the marginal probability of genotypes and report as GQ in each sample field in the VCF output. boolean_true
--debug Print debugging output. boolean_true
--dd Print more verbose debugging output boolean_true

Output

Name Description Attributes
--output Output directory file, example: "freebayes_out"
--vcf Output VCF-format results to FILE. string, example: "snp.vcf"

Authors

  • Xichen Wu (author)