HaplotypeCaller
Filtering by any of QUAL, DP, or GQ produced monotonic decreases in genotype mismatch rates with the HaplotypeCaller SNP set (Fig. 3, S14-16). These three filtering metrics would be useful for researchers unable to use VQSR and requiring further increased filtering stringency. The metrics FS, MQ, MQRankSum, QD, ReadPosRankSum, and SOR did not appreciably improve mismatch rates with further filtering, and in the case of QD slightly increased mismatch rates in our data (Fig. S17-22).