Varlap

Abstract

Varlap is primarily a quality control tool for genetic variants arising from high throughput DNA sequencing, where the variants have been called by aligning DNA sequencing reads to a reference genome. It takes as input a set of DNA variants and one or more BAM files. Varlap considers the genomic locus of each variant in each of the supplied BAM files and records information about the corresponding alignment context at that locus. For example, one of the metrics it calculates is the average edit distance of reads overlapping the variant locus. This can be a useful metric because regions with significantly higher average edit distance are more likely to contain erroneous variant calls. Varlap ..