2996693c9f
-- Old way (filtering for Q > 17 bases) resulted in biased FS when the site was good but there was a systematic shift in the QUAL of REF and ALT between strands of the reads (sometimes happens) -- New way (taking all bases) was consistent with BaseQualRankSum and other tests, but there can be a lot of low qual reference bases on one strand in some techs (ION/PROTON/PACBIO) because of the preference for introducing an indel vs. a mismatch. -- This implementation allows us to have our cake and eat it to by computing both p-values, and taking the maximum one (i.e., least significant). -- No integration tests updated yet -- still exploring the consequences of this change |
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