clintval / vartovcf / 37210193054

98%

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github

feat: add the LOW_DP and LOW_HICNT filters (#129)

LOW_DP, from --filter-low-dp, labels a call whose read depth (DP) is below the threshold, and LOW_HICNT, from --filter-low-hicnt, one with fewer high-quality ALT reads (HICNT) than the threshold, the count VarDict's own -r tests. VarDict normally drops such calls, but -p resets -r to 0. var2vcf_valid.pl applies these as d3 and v2, where v2 is described as "Var Depth" though it tests HICNT, and both are waived when HICNT x HIAF is at least 0.5; these labels have no waiver.

34 of 34 new or added lines in 2 files covered. (100.0%)

1084 of 1101 relevant lines covered (98.46%)

29.75 hits per line