Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.
Cutoff for Application of Yates Correction in Base Quality Recalibration
What is the criterion (or criteria) for applying the Yates correction to the empirical base qualities in the base quality recalibration?
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