Entering edit mode
10.0 years ago
devinliao0918
▴
40
Hi,
In the VCF files I have, the header says that output_mode=EMIT_VARIANTS_ONLY
. In this case, I see a lot of 0/1 and 1/1 genotypes in the files. However, I also see a few 0/0 genotypes and most of such 0/0 have very low qualities. I wonder how to interpret the 0/0 genotypes in the files?
Thanks for your comment.
These VCF files are individual VCF files as one file corresponds to one subject. You know, the
output_mode=EMIT_VARIANTS_ONLY
, so I expect to see none of0/0
genotype. Could you tell me why I still see few0/0
genotypes in such VCF files?I see. Now I better understand your question.
Do you see a pattern with the "culprit" descriptor on these
0/0
"variants"?So does that mean
0/0
is not an snp? Then why is it reported?