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BQSR directly in HaplotypeCaller

mnw21cammnw21cam Exeter UniversityMember ✭✭

I was wondering if GATK will behave correctly if I use the -BQSR option to HaplotypeCaller instead of PrintReads, thus saving a processing step in my pipeline. AFAIK, HaplotypeCaller is the only part of our pipeline that actually uses the base score values.

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