clintval / vartovcf / 37208705506

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github

feat: add the STRAND_BIAS filter (#126)

STRAND_BIAS, from --filter-strand-bias, labels a call whose ALT reads split across strands differently from its REF reads: the Fisher p-value of that table (STRAND_BIAS_FISHER_P) is below the threshold, optionally with the folded odds ratio of the same table above --filter-strand-bias-min-odds-ratio or an empty cell, and optionally with AF below --filter-strand-bias-max-af. Comparing ALT against REF keeps the test meaningful when every read is skewed toward one strand, as overlapping mates are under VarDict's -u. var2vcf_valid.pl's Bias additionally needs VarDict's 2;1 strand codes, which ALT can only reach with more than 12 reads, and an HIAF gate that insertions almost never pass.

93 of 93 new or added lines in 2 files covered. (100.0%)

1006 of 1023 relevant lines covered (98.34%)

28.63 hits per line