clintval / vartovcf / 37146114757

98%

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github

feat: add the LOW_MEAN_MAPQ filter (#122)

LOW_MEAN_MAPQ, from --filter-low-mean-mapq, labels a call whose ALT reads' mean mapping quality (MEAN_MAPQ) is below the threshold. var2vcf_valid.pl applies the same check as Q10, but only below an allele frequency of 0.8, a condition its description never states; this label has no such exemption. Labels are listed in a fixed order when a call fails several.

47 of 47 new or added lines in 2 files covered. (100.0%)

775 of 792 relevant lines covered (97.85%)

30.02 hits per line