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.

De novo quality scores

KathKath Posts: 36Member

Hello,

I was just wondering if anyone uses GATK's SelectVariants walker to call de novo mutations (Mendelian violations) and, if so, what -mvq cut-off do they use? My data is exome sequencing with a large range of read depths - from mean target coverage of 14X to >50X.

Thanks,

Kath

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