Author / Distributor
"See http://arxiv.org/abs/1207.3907 for an overview of the statistical models used in FreeBayes. Please cite this paper if you use FreeBayes in work that leads to publication"
"FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. It uses short-read alignments (BAM files
with Phred+33 encoded quality scores) for any number of individuals from a population and a reference genome to determine the most-likely combination of genotypes for the population at each position in a reference genome (FASTA). It reports positions which it finds to be more likely polymorphic than monomorphic in a standard variant interchange format (VCF). It can also use an input set of variants (VCF) as a source of prior information, and a copy number variant map (BED) to define non-uniform ploidy variation across the samples under analysis."
more details at freebayes
Also refer to Running Jobs on zcluster
/usr/local/freebayes/latest/ is pointed to the latest version at /usr/local/freebayes/0.9.6
Example running this at queue, shell script sub.sh
#!/bin/bash cd working_directory time /usr/local/freebayes/latest/bin/freebayes [options]
Example of submission to the queue:
qsub -q queueName ./sub.sh
for detailed help see Bfast
/usr/local/freebayes/latest/bin/freebayes -help usage: /usr/local/freebayes/latest/bin/freebayes [OPTION] ... [BAM FILE] ... Bayesian haplotype-based polymorphism discovery. citation: Erik Garrison, Gabor Marth "Haplotype-based variant detection from short-read sequencing" arXiv:1207.3907 (http://arxiv.org/abs/1207.3907) overview: To call variants from aligned short-read sequencing data, supply BAM files and a reference. FreeBayes will provide VCF output on standard out describing SNPs, indels, and complex variants in samples in the input alignments. By default, FreeBayes will consider variants supported by at least 2 observations in a single sample (-C) and also by at least 20% of the reads from a single sample (-F). These settings are suitable to low to high depth sequencing in haploid and diploid samples, but users working with polyploid or pooled samples may wish to adjust them depending on the characteristics of their sequencing data. FreeBayes is capable of calling variant haplotypes shorter than a read length where multiple polymorphisms segregate on the same read. The maximum distance between polymorphisms phased in this way is determined by the --max-complex-gap, which defaults to 3bp. In practice, this can comfortably be set to half the read length. Ploidy may be set to any level (-p), but by default all samples are assumed to be diploid. FreeBayes can model per-sample and per-region variation in copy-number (-A) using a copy-number variation map. parameters: -h --help Prints this help dialog. input and output: -b --bam FILE Add FILE to the set of BAM files to be analyzed. -c --stdin Read BAM input on stdin. -v --vcf FILE Output VCF-format results to FILE. -f --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. -t --targets FILE Limit analysis to targets listed in the BED-format FILE. -r --region <chrom>:<start_position>..<end_position> Limit analysis to the specified region, 0-base coordinates, end_position included. -s --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. -A --cnv-map FILE Read a copy number map from the BED file FILE, which has the format: reference sequence, start, end, sample name, copy number ... for each region in each sample which does not have the default copy number as set by --ploidy. -L --trace FILE Output an algorithmic trace to FILE. --failed-alleles FILE Write a BED file of the analyzed positions which do not pass --pvar to FILE. -@ --variant-input VCF Use variants reported in VCF file as input to the algorithm. Variants in this file will be treated as putative variants even if there is not enough support in the data to pass input filters. -l --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. --haplotype-basis-alleles VCF 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 At sites where genotypes are made over haplotype alleles, provide information about all alleles in output, not only those which are called. reporting: -P --pvar N Report sites if the probability that there is a polymorphism at the site is greater than N. default: 0.0. Note that post- filtering is generally recommended over the use of this parameter. -_ --show-reference-repeats Calculate and show information about reference repeats in the VCF output. population model: -T --theta N 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 default: 0.001 -p --ploidy N Sets the default ploidy for the analysis to N. default: 2 -J --pooled-discrete Assume that samples result from pooled sequencing. Model pooled samples using discrete genotypes across pools. When using this flag, set --ploidy to the number of alleles in each sample or use the --cnv-map to define per-sample ploidy. -K --pooled-continuous Output all alleles which pass input filters, regardles of genotyping outcome or model. reference allele: -Z --use-reference-allele This flag includes the reference allele in the analysis as if it is another sample from the same population. --reference-quality MQ,BQ Assign mapping quality of MQ to the reference allele at each site and base quality of BQ. default: 100,60 allele scope: -I --no-snps Ignore SNP alleles. -i --no-indels Ignore insertion and deletion alleles. -X --no-mnps Ignore multi-nuceotide polymorphisms, MNPs. -u --no-complex Ignore complex events (composites of other classes). -n --use-best-n-alleles N Evaluate only the best N SNP alleles, ranked by sum of supporting quality scores. (Set to 0 to use all; default: all) -E --max-complex-gap N Allow complex alleles with contiguous embedded matches of up to this length. indel realignment: -O --dont-left-align-indels Turn off left-alignment of indels, which is enabled by default. input filters: -4 --use-duplicate-reads Include duplicate-marked alignments in the analysis. default: exclude duplicates marked as such in alignments -m --min-mapping-quality Q Exclude alignments from analysis if they have a mapping quality less than Q. default: 0 -q --min-base-quality Q Exclude alleles from analysis if their supporting base quality is less than Q. default: 0 -R --min-supporting-allele-qsum Q Consider any allele in which the sum of qualities of supporting observations is at least Q. default: 0 -Y --min-supporting-mapping-qsum Q Consider any allele in which and the sum of mapping qualities of supporting reads is at least Q. default: 0 -Q --mismatch-base-quality-threshold Q Count mismatches toward --read-mismatch-limit if the base quality of the mismatch is >= Q. default: 10 -U --read-mismatch-limit N Exclude reads with more than N mismatches where each mismatch has base quality >= mismatch-base-quality-threshold. default: ~unbounded -z --read-max-mismatch-fraction N Exclude reads with more than N [0,1] fraction of mismatches where each mismatch has base quality >= mismatch-base-quality-threshold default: 1.0 -$ --read-snp-limit N Exclude reads with more than N base mismatches, ignoring gaps with quality >= mismatch-base-quality-threshold. default: ~unbounded -e --read-indel-limit N Exclude reads with more than N separate gaps. default: ~unbounded -0 --standard-filters Use stringent input base and mapping quality filters Equivalent to -m 30 -q 20 -R 0 -S 0 -x --indel-exclusion-window Ignore portions of alignments this many bases from a putative insertion or deletion allele. default: 0 -F --min-alternate-fraction N Require at least this fraction of observations supporting an alternate allele within a single individual in the in order to evaluate the position. default: 0.2 -C --min-alternate-count N Require at least this count of observations supporting an alternate allele within a single individual in order to evaluate the position. default: 2 -3 --min-alternate-qsum N Require at least this sum of quality of observations supporting an alternate allele within a single individual in order to evaluate the position. default: 0 -G --min-alternate-total N Require at least this count of observations supporting an alternate allele within the total population in order to use the allele in analysis. default: 1 -! --min-coverage N Require at least this coverage to process a site. default: 0 population priors: -k --no-population-priors Equivalent to --pooled-discrete and removal of Ewens Sampling Formula priors mappability priors: -w --hwe-priors-off Disable estimation of the probability of the combination arising under HWE given the allele frequency as estimated by observation frequency. -V --binomial-obs-priors-off Disable incorporation of prior expectations about observations. Uses read placement probability, strand balance probability, and read position (5'-3') probability. -a --allele-balance-priors-off Disable use of aggregate probability of observation balance between alleles as a component of the priors. genotype likelihoods: --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. algorithmic features: --report-genotype-likelihood-max Report genotypes using the maximum-likelihood estimate provided from genotype likelihoods. -M --site-selection-max-iterations N Uses hill-climbing algorithm to search posterior space for N iterations to determine if the site should be evaluated. Set to 0 to prevent use of this algorithm for site selection, and to a low integer for improvide site selection at a slight performance penalty. default: 5. -B --genotyping-max-iterations N Iterate no more than N times during genotyping step. default: 1000. --genotyping-max-banddepth N Integrate no deeper than the Nth best genotype by likelihood when genotyping. default: 6. -W --posterior-integration-limits N,M Integrate all genotype combinations in our posterior space which include no more than N samples with their Mth best data likelihood. default: 1,3. -N --exclude-unobserved-genotypes Skip sample genotypings for which the sample has no supporting reads. -S --genotype-variant-threshold N 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. default: ~unbounded -j --use-mapping-quality Use mapping quality of alleles when calculating data likelihoods. -H --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. -D --read-dependence-factor N Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations. default: 0.9 -= --genotype-qualities Calculate the marginal probability of genotypes and report as GQ in each sample field in the VCF output. debugging: -d --debug Print debugging output. -dd Print more verbose debugging output (requires "make DEBUG") author: Erik Garrison <firstname.lastname@example.org>, Marth Lab, Boston College, 2010-2012 date: 2013-01-28 version: 0.9.9
source from freebayes