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Min mapping quality for UnifiedGenotyper

indapaindapa Member
edited August 2012 in Ask the GATK 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.


  • 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_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    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.

  • marzimarzi netherlandsMember

    if I am right, MQ in VCF file is for filtering mapping quality, But MQ means Root Mean Square of the mapping quality, not mapping quality itself. So, if we use e.g 20 does it mean that I filtered mapping quality less than 20?

  • marzimarzi netherlandsMember

    Hi all,

    I used UG to call my snps. I got so many snps which is not expected. e.g for chr1 of layer chicken which is the largest chr I got 44 million snps. It means almost every positions was called as SNP. I could not find the problem. any idea will be appreciated.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    @marzi, it sounds like you may be using the wrong reference genome.

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