SNP calling inconsistency

GiulianoGiuliano Posts: 3Member

Hi to all,
I ran UnifiedGenotyper of three exome seq samples and phased with familial pedigree. During the manual filtration I saw several inconsistency. For example I get this output from UnifiedGenotyper and phasing:

chr2 38525498 rs76204302 T G 66.79 . AC=2;AF=0.333;AN=6;BaseQRankSum=-7.191;DB;DP=180;Dels=0.00;FS=208.951;HaplotypeScore=13.8978;MLEAC=2;MLEAF=0.333;MQ=60.00;MQ0=0;MQRankSum=2.030;QD=0.52;ReadPosRankSum=1.325;SB=-2.263e+00 GT:AD:DP:GQ:PL 0/0:30,22:52:39:0,39,729 0/1:9,7:16:5:5,0,280 0/1:55,57:112:98:98,0,1169

The order of samples are father, mother and son.How is possible that the father with, respectively 30 bases REF and 22 bases VAR is called 0/0?



  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 8,733Administrator, GATK Dev admin

    For issues with calls made by the UG, please read this FAQ article:

    Keep in mind that allele depths are unfiltered. I encourage you to look at the site in IGV to verify whether the call looks likely or not. If you still believe the call is problematic, please post a screenshot and supporting evidence, and we'll take a closer look.

    Also make sure that you are running the latest version (currently 2.4-3).

    Geraldine Van der Auwera, PhD

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