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Variants called with Allele Depth=0 and getting heterozygous genotype

Hi there,

I want to show an example of a confusing output.
I am doing variant analysis of exomes using trio data. This is a result after HaplotypeCaller, GenotypeGVCF, VariantFiltering, PhaseByTransmission:

chr15 99192754 . CTTTTTTTTT C 444.56 PASS BaseQRankSum=0.063;DP=75;FS=13.646;MLEAC=1;MLEAF=0.167;MQ=58.95;MQ0=0;MQRankSum=0.839;QD=29.64;ReadPosRankSum=0.467 GT:AD:GQ:PL:TP 0|1:8,0:81:81,0,267:13 0|0:4,0:13:0,13,134:13 1|0:2,13:99:252,0,175:13

For the first sample you can see that even if the ALT filtered reads are 0, the genotype called is 0/1. Why this happens?
I cannot understand well because when I read here (http://gatkforums.broadinstitute.org/gatk/discussion/1268/what-is-a-vcf-and-how-should-i-interpret-it) I pull out of this that AD (8,0) are unfiltered depths and GQ (81) should be a reliable value. But how can the algorithm be so sure with zero reads for the ALT allele?

Thank you for the nice program

Regards,

Francesco

Answers

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