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Dear GATK team,
Could you please help me how to explain genotyping in my vcf file. I have Illumina data and vcf caller was GATK. My variant frequency (Alt variant freq) is 99.7%. DP = 4622 (AD = 16, 4606) - so I would expect that this sample is alternate homozygous. But when I check PL value, which is - PL = 1655,0,323 - after calculating my likelihood -
REF= G ALT= A
P(D|GG) = 10 ^ -165.5 = small P(D|AG) = 10 ^ 0 = 1 P(D|AA) = 10 ^ 32.3 = small
we can see it is heterozygous. Can anybody help me how to interpret my result? How it is possible that likelihoods show me heterozygous and coverage and VF show me homozygous?
Here is part of my vcf file:
chr13 32899193 . G A 1625.01 PASS AC=1;AF=0.5;AN=2;DP=4622;QD=0.35;TI=NM_000059;GI=BRCA2;FC=Silent GT:AD:DP:GQ:PL:VF:GQX 0/1:16,4606:5000:99:1655,0,323:0.997:99
Thank you for any explanation.