clintval / vartovcf / 37210428804

98%

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github

feat: add the LOW_HICNT_FRACTION filter (#130)

LOW_HICNT_FRACTION, from --filter-low-hicnt-fraction, labels a call whose fraction of high-quality ALT reads (HICNT over AD[1]) is below the threshold. It is VarDict's own -o rule restated: high-quality over low-quality ALT reads below 1.5 is a high-quality fraction below 0.6, and -p turns that rule off. var2vcf_valid.pl applies it as SN1.5, described as signal to noise. Two filter fixture rows now carry a high-quality ALT count equal to their ALT count, so each still shows a single label.

23 of 23 new or added lines in 2 files covered. (100.0%)

1107 of 1124 relevant lines covered (98.49%)

30.0 hits per line