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Hard-Filtering odd MQ distributions

anapaulamachadoanapaulamachado LausanneMember
edited July 2018 in Ask the GATK team

I'm working on filtering my snp calls from a non-model organism and thus going with hard-filtering instead of VQSR. I know this is always a bit of touch-and-go and there's no definite answer to which thresholds to employ (I've been through the documentation) but I'm hoping you can give me some more pointers.

I've started by using your indications first except for QD, and based on missing data and coverage. So right now I have filtered SNPs with: QD < 5 ¦¦ FS < 60 ¦¦ MQ < 40 ¦¦ MQRankSum < -12.5 ¦¦ ReadPosRankSum < -8 ¦¦ SOR < 3, maximum 30% missing calls, resulting in 16'397'726 SNPs (of 19'047'259 total unfiltered calls).
These the distributions before and after filtering (QUAL just for indication, didn't apply any filter to it).

It looks considerable better to me, but still far from what your example data looks like. In particular, I'm wondering about my MQ distribution that has these very high values (over 400, some come as "Inf" even) - have you seen this before?
Further, would it be "ok" to filter on the upper value of MQ as well as the lowest? Thanks !


Best Answers

  • anapaulamachadoanapaulamachado Lausanne
    Accepted Answer

    I've tried running GenotypeGVCFs with GATK3.8.1 but the distributions have not changed. Guess it must be from versions 3 to 4 or when making the g.vcf. Unfortunately I cannot recreate all my gvcf cause I got some of them from a colleague. I'll try to make the time in the next few weeks to recreate the gvcf for my own samples with 3.8.1 and at least let you know if that's it or not.

    In any case, I selected these "too-high-MQ" calls and they look fine for all other indexes, no weird homo/heterozygosity, good QD/QUALS etc... I guess I'll just let it go and keep these variables, unless you see a problem with it.

    Thanks !

  • SheilaSheila Broad Institute admin
    Accepted Answer

    Hi Ana,

    I guess I'll just let it go and keep these variables, unless you see a problem with it.

    Yes, I think that is totally fine and probably the easiest in your case.



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