Small variants were called using the previously established GATK protocol [48]. Briefly, raw sequencing reads were trimmed and filtered using the Trimmomatic software [54]. Paired-end reads passing processing were then aligned to the GRCh38 human reference genome using Burrows-Wheeler Aligner, duplicates were marked with Picard, and alignment quality was improved using the Genome Analysis Toolkit [51] local realigner and base quality score recalibrator. Short somatic variants were then called using MuTect2 [55]. The analysis protocol with version information of all tools and details of reference datasets used in analyses have been explained earlier [48]. Following variant calling, variants were annotated with Annovar [56] and variants not passing all MuTect2 filters, falling into intronic and intergenic regions, classified as synonymous or non-frameshift variation, with an ExAC [57], ESP [58], 1KG [59] minor allele frequency higher than 1%, with a variant calling quality less than 40, residing in sites covered by less than 10 reads, with variant allele frequency less than 2% or higher than 30%, and with SNV strand-odd-ratio higher than 3 or indel strand-odd-ratio higher than 11 were removed.

AlleleDB is a repository, providing genomic annotation of cis-regulatory single nucleotide variants (SNVs) associated with allele-specific binding (ASB) and expression (ASE).

Introduction to Population Genetics