Workflow from Scientific Research

Workflow of the variant calling approach in VNTR regions from short-read sequencing data: the input file is provided in BAM format, with reads aligned to the reference genome (step 1); the region of interest (ROI) defined by the user (provided as, e.g., BED file) is selected (step 2); the VNTR reads are extracted from the provided ROI (step 3); the extracted reads are realigned to one reference repeat (step 4) for variant calling with mutserve (step 5), resulting in a VCF output file that can subsequently be annotated (see GitHub repository in the Availability of data and materials section)

DOI