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).