Why DP and GT info in my VCF file are inconsistent?
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5.2 years ago
Makplus T ▴ 100

Here is part of my VCF file with two samples:

GT:AD:AF:DP:F1R2:F2R1:SB
0/1:73,4:0.061:77:27,1:46,3:31,42,2,2
0/0:333,23:0.065:356:160,8:166,15:155

I understand that GT stands for genotype, so, 0/1 means heterozygote and 73 reads support ref allele and 4 reads support alt allele

What puzzles me is : when turn to the other sample, '0/0' seems it is homozygous genotype. but the AD info is '333,23', Does it mean 333 reads for ref and 23 reads for alt allele?

GATK VCF format • 1.2k views
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Does it mean 333 reads for ref and 23 reads for alt allele?

yes

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Thank you. And this is my puzzle, if the genotype is '0/0' , Why there are 23 reads for alt allele?

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