CEGH-Filter

Flagging algorithm with criteria based on depth of coverage (≥10 reads) and allele balance [between 0.3 and 0.7 (heterozygous), below 0.1 (reference homozygous) and above 0.9 (alternate homozygous) proportion of reference allele over the sum of reference and alternate]. Two cutoffs were used: the proportion of alternate genotypes that don’t fit criteria among all alternate genotypes and the total number of genotypes that fit criteria. 100% proportion: FDP (>50% of called genotypes haven’t met minimum depth) or FAB (≤50% were flagged as low DP, therefore most genotypes were off allele balance thresholds); ≥50%: WK (≥500 genotypes) or WK-LowCall (<500 genotypes); from 10-50%: SR (≥500 genotypes) or SR-LowCall (<500 genotypes); ≤ 10% vSR (≥500 genotypes) or vSR-LowCall (<500 genotypes). Variants with vSR, SR, WK, vSR-LowCall, SR-LowCall and WK-LowCall flags are probably true, with varying levels of confidence. Threshold for genotype counts that fit criteria in [SABE-609-WES] was set in 250. Variants with FDP or FAB are probably false (although called, no variants met criteria). FAB is checked only after FDP was applied. Multiallelic variants were split, but genotypes other than 0/0, 0/1 and 1/1 were not included in this preliminary analysis.