usage: freebayes [OPTION] ... [BAM FILE] ... Bayesian small polymorphism discovery. 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 :.. Limit analysis to the specified region, 0-base coordinates, end_position not included (same as BED format). -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. -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. A report will be generated for every record in the VCF file. -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. reporting: -P --pvar N Report sites if the probability that there is a polymorphism at the site is greater than N. default: 0.0001 -_ --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 Assume that samples result from pooled sequencing. When using this flag, set --ploidy to the number of alleles in each sample. 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. -H --diploid-reference If using the reference sequence as a sample (default), treat it as diploid. default: false (reference is haploid) --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 --left-align-indels Left-realign and merge gaps embedded in reads. default: false input filters: -4 --use-duplicate-reads Include duplicate-marked alignments in the analysis. default: exclude duplicates -m --min-mapping-quality Q Exclude alignments from analysis if they have a mapping quality less than Q. default: 30 -q --min-base-quality Q Exclude alleles from analysis if their supporting base quality is less than Q. default: 20 -R --min-supporting-quality MQ,BQ In order to consider an alternate allele, at least one supporting alignment must have mapping quality MQ, and one supporting allele must have base quality BQ. default: 0,0, unset -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 --no-filters Do not use any input base and mapping quality filters Equivalent to -m 0 -q 0 -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: 0.0 -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: 1 -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 bayesian priors: -Y --no-ewens-priors Turns off the Ewens' Sampling Formula component of the priors. -k --no-population-priors Equivalent to --pooled --no-ewens-priors -w --hwe-priors Use the probability of the combination arising under HWE given the allele frequency as estimated by observation frequency. observation prior expectations: -V --binomial-obs-priors Incorporate expectations about osbervations into the priors, Uses read placement probability, strand balance probability, and read position (5'-3') probability. -a --allele-balance-priors Use aggregate probability of observation balance between alleles as a component of the priors. Best for observations with minimal inherent reference bias. algorithmic features: -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: 25. -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. -K --no-permute Do not scale prior probability of genotype combination given allele frequency by the number of permutations of included genotypes. -^ --genotype-combo-step-max N When generating genotype combinations, do not include genotypes where the genotype data likelihood is log(N) from the highest likelihood genotype for that individual. default: ~unbounded -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. -D --read-dependence-factor N Incorporate non-independence of reads by scaling successive observations by this factor during data likelihood calculations. default: 0.9 -= --no-marginals Do not calculate the marginal probability of genotypes. Saves time and improves scaling performance in large populations. debugging: -d --debug Print debugging output. -dd Print more verbose debugging output (requires "make DEBUG") author: Erik Garrison , Marth Lab, Boston College, 2010, 2011 date: 2011-09-08 version: 0.9.0