clintval / vartovcf / 37142524128

98%

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github

feat: write VarDict's realigned-read fraction as FORMAT REALIGNED_FRAC_OF_DP (#113)

VarDict's ExtraAF column, which var2vcf_valid.pl writes as INFO ADJAF and describes as an adjusted AF, is the number of reads VarDict reassigned to the ALT allele by local realignment or MNV merging divided by its depth denominator. Those reads are already counted in the ALT depth and AF, so the value is the share of depth that realignment contributed, not an adjusted AF. It is now FORMAT REALIGNED_FRAC_OF_DP (Number=A), copied from VarDict's 4-decimal value and missing when there is no ALT allele.

8 of 8 new or added lines in 2 files covered. (100.0%)

587 of 603 relevant lines covered (97.35%)

28.07 hits per line