Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Skip non-diploid or other invalid variants instead of raising error #128

Open
pontushojer opened this issue Jan 13, 2023 · 0 comments
Open

Comments

@pontushojer
Copy link
Contributor

I run into this error when running extractHairs

ERROR: Non-diploid VCF entry detected. Each VCF entry must have a diploid genotype (GT) field consisting of two 
alleles in the set {0,1,2} separated by either '/' or '|'. For example, "1/1", "0/1", and "0|2" are valid diploid 
genotypes for HapCUT2, but "1", "0/3", and "0/0/1" are not.
The invalid entry is: 

chr1    1396190 .       GAA     G,GA,GAAA       22.10   PASS    .       GT:GQ:DP:AD:VAF:PL      1/3:2:34:7,5,4,9:0.147059,0.117647,0.264706:16,1,37,2,34,34,2,0,2,29

Would it be possible to instead of raising an error here, just skipping these invalid variants. Maybe just output a warning instead. Since I would need to go back and filter out this variant its a bit annoying for the program to stop here.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant