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. Author manuscript; available in PMC: 2022 Aug 7.
Published in final edited form as: Nat Biotechnol. 2022 Feb 7;40(5):672–680. doi: 10.1038/s41587-021-01158-1

Figure 5:

Figure 5:

The new CMRG small variant benchmark includes more challenging variants and identifies more false negatives in a standard short-read callset (Illumina-bwamem-GATK) than the previous v4.2.1 benchmark in these challenging genes. While the false negative rate (circles) is similar in easier regions (purple “Not In All Difficult” points), the false negative rate is much higher overall (green “All CMRG Benchmark Regions” points). The fraction of variants excluded from the benchmark regions (triangles) is much higher for the v4.2.1 benchmark in all stratifications. This information is also presented in “summary stats NYGC” in Supplementary Data 4.