Finding SNPs and INDELs from sequence data using VariantTools

A key bioinformatics task is to take an alignment of high-throughput sequence reads, typically stored in a BAM file, and compute a list of variant positions. Of course, this is ably handled by many external command-line programs and tools and usually results in a VCF file of variants, but some really powerful packages in Bioconductor can do the whole thing, quickly and efficiently, by taking advantage of BiocParallel’s facilities for parallel evaluation, a set of tools designed to speed up work with large datasets in Bioconductor objects. Using Bioconductor tools allows us to keep all of our processing steps within R, and in this recipe, we’ll go through a whole pipeline – from reads to lists of genes carrying variants – using purely R code and several Bioconductor packages.