![]() ![]() ![]() Our tools are part of the wider bioinformatics ecosystem and we highlight best practices. These tools run everyday in critical biomedical pipelines and countless shell scripts. These tools are applied for comparison, filtering, normalisation, smoothing and annotation of VCF, as well as output of statistics, visualisation, and transformations of files variants. Here we present a spectrum of over 125 useful, complimentary free and open source software tools and libraries, we wrote and made available through the multiple vcflib, bio-vcf, cyvcf2, hts-nim and slivar projects. The VCF format can represent single nucleotide variants, multi-nucleotide variants, insertions and deletions, and simple structural variants called and anchored against a reference genome. Since its introduction in 2011 the variant call format (VCF) has been widely adopted for processing DNA and RNA variants in practically all population studies-as well as in somatic and germline mutation studies.
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