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.

Min mapping quality for UnifiedGenotyper

indapaindapa Posts: 1Member
edited August 2012 in Ask the team

HI GATK - I am still using the GenomeAnalysisTK-1.6-5-g557da77 version for UnifiedGenotyper. This is probably a silly question, but is there a way to set a parameter for minimum mapping quality score for reads, in deciding whether to evaluate them for variant detection. I know there is a --min_base_quality_score parameter, but I don't see on for mapping quality. http://www.broadinstitute.org/gsa/gatkdocs/release/org_broadinstitute_sting_gatk_walkers_genotyper_UnifiedGenotyper.html

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