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vcflib(1) vcflib (index) vcflib(1) NAME vcflib index DESCRIPTION vcflib contains tools and libraries for dealing with the Variant Call Format (VCF) which is a flat-file, tab-delimited textual format intend- ed to describe reference-indexed variations between individuals. VCF provides a common interchange format for the description of varia- tion in individuals and populations of samples, and has become the de- facto standard reporting format for a wide array of genomic variant de- tectors. vcflib provides methods to manipulate and interpret sequence variation as it can be described by VCF. It is both: • an API for parsing and operating on records of genomic variation as it can be described by the VCF format, • and a collection of command-line utilities for executing complex ma- nipulations on VCF files. The API itself provides a quick and extremely permissive method to read and write VCF files. Extensions and applications of the library pro- vided in the included utilities (*.cpp) comprise the vast bulk of the library's utility for most users. filter filter command description -------------------------------------------------------------------------- vcffilter VCF filter the specified vcf file using the set of filters vcfuniq List unique genotypes. Simi- lar to GNU uniq, but aimed at VCF records. vcfuniq removes records which have the same position, ref, and alt as the previous record on a sorted VCF file. Note that it does not adjust/combine genotypes in the output, but simply takes the first record. See also vcfcreatemulti for com- bining records. vcfuniqalleles List unique alleles For each record, remove any duplicate alternate alleles that may have resulted from merging separate VCF files. metrics metrics command description -------------------------------------------------------------------------- vcfcheck Validate integrity and identi- ty of the VCF by verifying that the VCF record's REF matches a given reference file. vcfdistance Adds a tag to each variant record which indicates the distance to the nearest vari- ant. (defaults to BasesTo- ClosestVariant if no custom tag name is given. vcfentropy Annotate VCF records with the Shannon entropy of flanking sequence. Anotates the output VCF file with, for each record, EntropyLeft, Entropy- Right, EntropyCenter, which are the entropies of the se- quence of the given window size to the left, right, and center of the record. Also adds EntropyRef and EntropyAlt for each alt. vcfhetcount Calculate the heterozygosity rate: count the number of al- ternate alleles in heterozy- gous genotypes in all records in the vcf file vcfhethomratio Generates the het/hom ratio for each individual in the file phenotype phenotype command description -------------------------------------------------------------------------- permuteGPAT++ permuteGPAT++ is a method for adding empirical p-values to a GPAT++ score. genotype genotype command description -------------------------------------------------------------------------- abba-baba abba-baba calculates the tree pattern for four indviduals. This tool assumes reference is ancestral and ignores non ab- ba-baba sites. The output is a boolian value: 1 = true , 0 = false for abba and baba. the tree argument should be specified from the most basal taxa to the most derived. hapLrt HapLRT is a likelihood ratio test for haplotype lengths. The lengths are modeled with an exponential distribution. The sign denotes if the target has longer haplotypes (1) or the background (-1). normalize-iHS normalizes iHS or XP-EHH scores. transformation transformation command description -------------------------------------------------------------------------- dumpContigsFromHeader Dump contigs from header smoother smoothes is a method for win- dow smoothing many of the GPAT++ formats. vcf2dag Modify VCF to be able to build a directed acyclic graph (DAG) vcf2fasta Generates sample_seq:N.fa for each sample, reference se- quence, and chromosomal copy N in [0,1... ploidy]. Each se- quence in the fasta file is named using the same pattern used for the file name, allow- ing them to be combined. vcf2tsv Converts VCF to per-allelle or per-genotype tab-delimited format, using null string to replace empty values in the table. Specifying -g will output one line per sample with genotype information. When there is more than one alt allele there will be mul- tiple rows, one for each al- lele and, the info will match the `A' index vcfaddinfo Adds info fields from the sec- ond file which are not present in the first vcf file. vcfafpath Display genotype paths vcfallelicprimitives WARNING: this tool is consid- ered legacy and is only re- tained for older workflows. It will emit a warning! Even though it can use the WFA you should use vcfwave instead. vcfannotate Intersect the records in the VCF file with targets provided in a BED file. Intersections are done on the reference se- quences in the VCF file. If no VCF filename is specified on the command line (last ar- gument) the VCF read from stdin. vcfannotategenotypes Examine genotype correspon- dence. Annotate genotypes in the first file with genotypes in the second adding the geno- type as another flag to each sample filed in the first file. annotation-tag is the name of the sample flag which is added to store the annota- tion. also adds a `has_vari- ant' flag for sites where the second file has a variant. vcfbreakmulti If multiple alleles are speci- fied in a single record, break the record into multiple lines, preserving allele-spe- cific INFO fields. vcfcat Concatenates VCF files vcfclassify Creates a new VCF where each variant is tagged by allele class: snp, ts/tv, indel, mnp vcfcleancomplex Removes reference-matching se- quence from complex alleles and adjusts records to reflect positional change. vcfcombine Combine VCF files positional- ly, combining samples when sites and alleles are identi- cal. Any number of VCF files may be combined. The INFO field and other columns are taken from one of the files which are combined when records in multiple files match. Alleles must have identical ordering to be com- bined into one record. If they do not, multiple records will be emitted. vcfcommonsamples Generates each record in the first file, removing samples not present in the second vcfcreatemulti Go through sorted VCF and when overlapping alleles are repre- sented across multiple records, merge them into a single multi-ALT record. See the documentation for more in- formation. vcfecho Echo VCF to stdout (simple de- mo) vcfevenregions Generates a list of regions, e.g. chr20:10..30 using the variant density information provided in the VCF file to ensure that the regions have even numbers of variants. This can be use to reduce the variance in runtime when di- viding variant detection or genotyping by genomic coordi- nates. vcffixup Generates a VCF stream where AC and NS have been generated for each record using sample genotypes vcfflatten Removes multi-allelic sites by picking the most common alter- nate. Requires allele fre- quency specification `AF' and use of `G' and `A' to specify the fields which vary accord- ing to the Allele or Genotype. VCF file may be specified on the command line or piped as stdin. vcfgeno2alleles modifies the genotypes field to provide the literal alleles rather than indexes vcfgeno2haplo Convert genotype-based phased alleles within -window-size into haplotype alleles. Will break haplotype construction when encountering non-phased genotypes on input. vcfgenosamplenames Get samplenames vcfglbound Adjust GLs so that the maximum GL is 0 by dividing all GLs for each sample by the max. vcfglxgt Set genotypes using the maxi- mum genotype likelihood for each sample. vcfindex Adds an index number to the INFO field (id=position) vcfinfo2qual Sets QUAL from info field tag keyed by [key]. The VCF file may be omitted and read from stdin. The average of the field is used if it contains multiple values. vcfinfosummarize Take annotations given in the per-sample fields and add the mean, median, min, or max to the site-level INFO. vcfintersect VCF 1.0.12 set analysis vcfkeepgeno Reduce file size by removing FORMAT fields not listed on the command line from sample specifications in the output vcfkeepinfo To decrease file size remove INFO fields not listed on the command line vcfkeepsamples outputs each record in the vcf file, removing samples not listed on the command line vcfld Compute LD vcfleftalign Left-align indels and complex variants in the input using a pairwise ref/alt alignment followed by a heuristic, iter- ative left realignment process that shifts indel representa- tions to their absolute left- most (5') extent. vcflength Add length info field vcfnullgenofields Makes the FORMAT for each variant line the same (uses all the FORMAT fields de- scribed in the header). Fills out per-sample fields to match FORMAT. Expands GT values of `.' with number of alleles based on ploidy (eg: `./.' for dipolid). vcfnumalt outputs a VCF stream where NU- MALT has been generated for each record using sample geno- types vcfoverlay Overlay records in the input vcf files with order as prece- dence. vcfprimers For each VCF record, extract the flanking sequences, and write them to stdout as FASTA records suitable for align- ment. vcfqual2info Puts QUAL into an info field tag keyed by [key]. vcfremap For each alternate allele, at- tempt to realign against the reference with lowered gap open penalty. If realignment is possible, adjust the cigar and reference/alternate alle- les. Observe how different alignment parameters, includ- ing context and entropy-depen- dent ones, influence variant classification and interpreta- tion. vcfremoveaberrantgenotypes strips samples which are ho- mozygous but have observations implying heterozygosity. Re- move samples for which the re- ported genotype (GT) and ob- servation counts disagree (AO, RO). vcfremovesamples outputs each record in the vcf file, removing samples listed on the command line vcfsample2info Take annotations given in the per-sample fields and add the mean, median, min, or max to the site-level INFO. vcfsamplediff Establish putative somatic variants using reported dif- ferences between germline and somatic samples. Tags each record where the listed sample genotypes differ with . The first sample is assumed to be germline, the second somatic. Each record is tagged with ={germline,somatic,loh} to specify the type of variant given the genotype difference between the two samples. vcfsamplenames List sample names vcfstreamsort Sorts the input (either stdin or file) using a streaming sort algorithm. Guarantees that the positional order is correct provided out-of-order variants are no more than 100 positions in the VCF file apart. vcfwave Realign reference and alter- nate alleles with WFA, parsing out the `primitive' alleles into multiple VCF records. New records have IDs that ref- erence the source record ID. Genotypes/samples are handled correctly. Deletions generate haploid/missing genotypes at overlapping sites. statistics statistics command description -------------------------------------------------------------------------- bFst bFst is a Bayesian approach to Fst. Importantly bFst ac- counts for genotype uncertain- ty in the model using genotype likelihoods. For a more de- tailed description see: `A Bayesian approach to inferring population structure from dom- inant markers' by Holsinger et al. Molecular Ecology Vol 11, issue 7 2002. The likelihood function has been modified to use genotype likelihoods pro- vided by variant callers. There are five free parameters estimated in the model: each subpopulation's allele fre- quency and Fis (fixation in- dex, within each subpopula- tion), a free parameter for the total population's allele frequency, and Fst. genotypeSummary Generates a table of genotype counts. Summarizes genotype counts for bi-allelic SNVs and indel iHS iHS calculates the integrated haplotype score which measures the relative decay of extended haplotype homozygosity (EHH) for the reference and alterna- tive alleles at a site (see: voight et al. 2006, Spiech & Hernandez 2014). meltEHH pFst pFst is a probabilistic ap- proach for detecting differ- ences in allele frequencies between two populations. pVst pVst calculates vst, a measure of CNV stratification. permuteSmooth permuteSmooth is a method for adding empirical p-values smoothed wcFst scores. plotHaps plotHaps provides the format- ted output that can be used with `bin/plotHaplotypes.R'. popStats General population genetic statistics for each SNP segmentFst segmentFst creates genomic segments (bed file) for re- gions with high wcFst segmentIhs Creates genomic segments (bed file) for regions with high wcFst sequenceDiversity The sequenceDiversity program calculates two popular metrics of haplotype diversity: pi and extended haplotype homozygo- isty (eHH). Pi is calculated using the Nei and Li 1979 for- mulation. eHH a convenient way to think about haplotype diversity. When eHH = 0 all haplotypes in the window are unique and when eHH = 1 all haplotypes in the window are identical. vcfaltcount count the number of alternate alleles in all records in the vcf file vcfcountalleles Count alleles vcfgenosummarize Adds summary statistics to each record summarizing quali- ties reported in called geno- types. Uses: RO (reference observation count), QR (quali- ty sum reference observations) AO (alternate observation count), QA (quality sum alter- nate observations) vcfgenotypecompare adds statistics to the INFO field of the vcf file describ- ing the amount of discrepancy between the genotypes (GT) in the vcf file and the genotypes reported in the . use this after vcfannotategenotypes to get correspondence statistics for two vcfs. vcfgenotypes Report the genotypes for each sample, for each variant in the VCF. Convert the numeri- cal represenation of genotypes provided by the GT field to a human-readable genotype for- mat. vcfparsealts Alternate allele parsing method. This method uses pairwise alignment of REF and ALTs to determine component allelic primitives for each alternate allele. vcfrandom Generate a random VCF file vcfrandomsample Randomly sample sites from an input VCF file, which may be provided as stdin. Scale the sampling probability by the field specified in KEY. This may be used to provide uniform sampling across allele fre- quencies, for instance. vcfroc Generates a pseudo-ROC curve using sensitivity and speci- ficity estimated against a pu- tative truth set. Threshold- ing is provided by successive QUAL cutoffs. vcfsitesummarize Summarize by site vcfstats Prints statistics about vari- ants in the input VCF file. wcFst wcFst is Weir & Cockerham's Fst for two populations. Neg- ative values are VALID, they are sites which can be treated as zero Fst. For more infor- mation see Evolution, Vol. 38 N. 6 Nov 1984. Specifically wcFst uses equations 1,2,3,4. SOURCE CODE See the source code repository at https://github.com/vcflib/vcflib CREDIT Citations are the bread and butter of Science. If you are using this software in your research and want to support our future work, please cite the following publication: Please cite: A spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar (https://jour- nals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009123). Garrison E, Kronenberg ZN, Dawson ET, Pedersen BS, Prins P (2022), PLoS Comput Biol 18(5): e1009123. https://doi.org/10.1371/jour- nal.pcbi.1009123 LICENSE Copyright 2011-2025 (C) Erik Garrison and vcflib contributors. Copy- right 2020-2025 (C) Pjotr Prins MIT licensed. AUTHORS Erik Garrison and vcflib contributors. vcflib vcflib(1)
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