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# vcflib ### A C++ library for parsing and manipulating VCF files. #### author: Erik Garrison <erik.garrison@bc.edu> #### license: MIT [](https://gitter.im/ekg/vcflib?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) [](https://travis-ci.org/vcflib/vcflib) --- ## overview The [Variant Call Format (VCF)](http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41) is a flat-file, tab-delimited textual format intended to concisely describe reference-indexed variations between individuals. VCF provides a common interchange format for the description of variation in individuals and populations of samples, and has become the _defacto_ standard reporting format for a wide array of genomic variant detectors. 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 manipulations 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 provided in the included utilities (*.cpp) comprise the vast bulk of the library's utility for most users. ## download and install 1. Under the repository name, click to copy the clone URL for the repository.  2. Go to the location where you want the cloned directory to be made: `cd <PathWhereIWantToCloneVcflib>` 3. Type `git clone --recursive`, and then paste the URL you copied in Step 1. 4. Enter the cloned directory and type `make` to compile the programs. If you want to use threading type `make openmp` instead of `make`. Only a few VCFLIB tools are threaded. 5. Once make is finished the executables are ready in the folder `<PathWhereIWantToCloneVcflib>/vcflib/bin/`. Set this path as an environment variable in the .bashrc file to access executables form everywhere on your proile OR call the executables from the path where they are. ## usage vcflib provides a variety of functions for VCF manipulation: ### comparison * Generate **haplotype-aware intersections** ([vcfintersect](#vcfintersect) -i), **unions** (vcfintersect -u), and **complements** (vcfintersect -v -i). * **Overlay-merge** multiple VCF files together, using provided order as precedence ([vcfoverlay](#vcfoverlay)). * **Combine** multiple VCF files together, handling samples when alternate allele descriptions are identical ([vcfcombine](#vcfcombine)). * **Validate** the integrity and identity of the VCF by verifying that the VCF record's REF matches a given reference file ([vcfcheck](#vcfcheck)). ### format conversion * Convert a VCF file into a per-allele or per-genotype **tab-separated (.tsv)** file ([vcf2tsv](#vcf2tsv)). * Store a VCF file in an **SQLite3** database (vcf2sqlite.py). * Make a **BED file** from the intervals in a VCF file (vcf2bed.py). ### filtering and subsetting * **Filter** variants and genotypes using arbitrary expressions based on values in the INFO and sample fields ([vcffilter](#vcffilter)). * **Randomly sample** a subset of records from a VCF file, given a rate ([vcfrandomsample](#vcfrandomsample)). * **Select variants** of a certain type (vcfsnps, vcfbiallelic, vcfindels, vcfcomplex, etc.) ### annotation * **Annotate** one VCF file with fields from the INFO column of another, based on position ([vcfaddinfo](#vcfaddinfo), [vcfintersect](#vcfintersect)). * Incorporate annotations or targets provided by a *BED* file ([vcfannotate](#vcfannotate), [vcfintersect](#vcfintersect)). * Examine **genotype correspondence** between two VCF files by annotating samples in one file with genotypes from another ([vcfannotategenotypes](#vcfannotategenotypes)). * Annotate variants with the **distance** to the nearest variant ([vcfdistance](#vcfdistance)). * Count the number of alternate alleles represented in samples at each variant record ([vcfaltcount](#vcfaltcount)). * **Subset INFO fields** to decrease file size and processing time ([vcfkeepinfo](#vcfkeepinfo)). * Lighten up VCF files by keeping only a **subset of per-sample information** ([vcfkeepgeno](#vcfkeepgeno)). * **Numerically index** alleles in a VCF file ([vcfindex](#vcfindex)). ### samples * Quickly obtain the **list of samples** in a given VCF file ([vcfsamplenames](#vcfsamplenames)). * **Remove samples** from a VCF file ([vcfkeepsamples](#vcfkeepsamples), [vcfremovesamples](#vcfremovesamples)). ### ordering * **Sort variants** by genome coordinate ([vcfstreamsort](#vcfstreamsort)). * **Remove duplicate** variants in vcfstreamsort'ed files according to their REF and ALT fields ([vcfuniq](#vcfuniq)). ### variant representation * **Break multiallelic** records into multiple records ([vcfbreakmulti](#vcfbreakmulti)), retaining allele-specific INFO fields. * **Combine overlapping biallelic** records into a single record ([vcfcreatemulti](#vcfcreatemulti)). * **Decompose complex variants** into a canonical SNP and indel representation ([vcfallelicprimitives](#vcfallelicprimitives)), generating phased genotypes for available samples. * **Reconstitute complex variants** provided a phased VCF with samples ([vcfgeno2haplo](#vcfgeno2haplo)). * **Left-align indel and complex variants** ([vcfleftalign](#vcfleftalign)). ### genotype manipulation * **Set genotypes** in a VCF file provided genotype likelihoods in the GL field ([vcfglxgt](#vcfglxgt)). * Establish putative **somatic variants** using reported differences between germline and somatic samples ([vcfsamplediff](#vcfsamplediff)). * Remove samples for which the reported genotype (GT) and observation counts disagree (AO, RO) ([vcfremoveaberrantgenotypes](#vcfremoveaberrantgenotypes)). ### interpretation and classification of variants * Obtain aggregate **statistics** about VCF files ([vcfstats](#vcfstats)). * Print the **receiver-operating characteristic (ROC)** of one VCF given a truth set ([vcfroc](#vcfroc)). * Annotate VCF records with the **Shannon entropy** of flanking sequence ([vcfentropy](#vcfentropy)). * Calculate the heterozygosity rate ([vcfhetcount](#vcfhetcount)). * Generate potential **primers** from VCF records ([vcfprimers](#vcfprimers)), to check for genome uniqueness. * Convert the numerical represenation of genotypes provided by the GT field to a **human-readable genotype format** ([vcfgenotypes](#vcfgenotypes)). * Observe how different alignment parameters, including context and entropy-dependent ones, influence **variant classification and interpretation** ([vcfremap](#vcfremap)). * **Classify variants** by annotations in the INFO field using a self-organizing map ([vcfsom](#vcfsom)); **re-estimate their quality** given known variants. A number of "helper" perl and python scripts (e.g. vcf2bed.py, vcfbiallelic) further extend functionality. In practice, users are encouraged to drive the utilities in the library in a streaming fashion, using pipes, to fully utilize resources on multi-core systems during interactive work. Piping provides a convenient method to interface with other libraries (vcf-tools, BedTools, GATK, htslib, bcftools, freebayes) which interface via VCF files, allowing the composition of an immense variety of processing functions. ## development See src/vcfecho.cpp for basic usage. src/Variant.h and src/Variant.cpp describe methods available in the API. vcflib is incorporated into several projects, such as [freebayes](https://github.com/ekg/freebayes), which may provide a point of reference for prospective developers. Additionally, developers should be aware of that vcflib contains submodules (git repositories) comprising its dependencie