Hello biostars!
I coded this set of programs to help groups dealing with genotypes/variant data/allele counts and need to store, analyze, filter and export that data to various formats used by pop. gen. software. It used bgzipped/binary files designed to store genotype likelihoods or allele counts. The design was heavily influenced by the bam format. I hope more people will jump on board and I welcome pull requests if you feel something is missing or suboptimal.
Description
Analysis of nuclear genomes often involves combining genotyping information from various individuals or populations to compute summary statistics or exporting them to various file formats (EIGENSTRAT, PLINK, etc..). This is achieved by parsing of multiple genotyping files (ex: VCF/BCF) to combined sets which are later exported to various formats or are used to compute summary statistics. Often, information such as ancestral allele information is also added.
Research groups usually do this by coding custom scripts tailored to the task at hand. New group members often cannot reproduce the analyses that were performed and often code their own scripts from scratch. This leads to time being wasted and an overall lack of reproducibility.
glactools are a set or programs coded in C++ designed to extract allele counts from VCF files (or the raw base count from BAM files) and store it as an intermediate representation, compute summary statistics and export it to various file formats used by population genetics software.
Website
https://grenaud.github.io/glactools/
Reference
Please find the version which will appear in Bioinformatics:
