UnifiedGenotyper
Filtering by any of QUAL, DP, or GQ resulted in decreased genotype mismatch rates with increasing stringency in the UnifiedGenotyper SNP set (Fig. 3, S26-28). As with HaplotypeCaller, these three filtering metrics would be useful for researches unable to filter with VQSR and requiring further filtering stringency. Similar to HaplotypeCaller, none of FS, MQ, MQRankSum, QD, ReadPosRankSum, nor SOR appreciably improved mismatch rates, and with our dataset filtering by QD or SOR slightly increased mismatch rates with UnifiedGenotyper (Fig. S29-34).