Question: Why DP and GT info in my VCF file are inconsistent?
0
gravatar for Makplus T
13 months ago by
Makplus T70
Makplus T70 wrote:

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?

format gatk vcf • 277 views
ADD COMMENTlink modified 12 months ago by Biostar ♦♦ 20 • written 13 months ago by Makplus T70

Does it mean 333 reads for ref and 23 reads for alt allele?

yes

ADD REPLYlink written 12 months ago by Pierre Lindenbaum130k

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

ADD REPLYlink written 12 months ago by Makplus T70
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