clintval / vartovcf / 37209135639

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github

feat: add the LOW_AF filter (#127)

LOW_AF, from --filter-low-af, labels a call whose AF (FORMAT AF) is below the threshold. VarDict normally drops such calls itself with -f, but in pileup mode (-p) it resets -f and -r and keeps every candidate, so this label is how low-AF candidates get marked there. var2vcf_valid.pl applies the same rule as f<min_af>, on VarDict's 4-decimal AF.

22 of 22 new or added lines in 2 files covered. (100.0%)

1028 of 1045 relevant lines covered (98.37%)

28.93 hits per line