Min mapping quality for UnifiedGenotyper

indapa

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

katiefs

Hello,

I have this same question. I'm also curious what the minimum mapping quality currently is for Unified Genotyper to consider a read. I see that it will not consider reads with unknown mapping quality, but so far I have not been able to find a minimum value written anywhere. Apologies if I've missed it.

Thanks a lot!

Geraldine_VdAuwera

By default by the UG does not look at reads that have unknown or zero mapping quality (using read filters as detailed here, but it does not apply a minimum mapping quality threshold as such. If you want to do that (although we prefer to filter after calling rather than impose pre-calling thresholds) you can use the MappingQuality filter.