We used the following QC filters: a (1) quality-score-vs.-depth filter, which excludes variants whose depth-normalized discovery confidence does not exceed 2.0; (2) a homopolymer-run filter, which excludes variants that have an alternate allele that matches the allele in an immediately adjacent homopolymer-run of length greater than 5; (3) a strand-bias filter, which excludes variants whose alternate allele is preferentially found on one of the two available read orientations at the site, and (4) an indel-mask filter, which excludes variants discovered at sites that overlap with indels.
