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

Midifying script for GT:DP:AD:GQ:PL:RNC genotype format #1

Open
gsa3 opened this issue Feb 17, 2023 · 0 comments
Open

Midifying script for GT:DP:AD:GQ:PL:RNC genotype format #1

gsa3 opened this issue Feb 17, 2023 · 0 comments

Comments

@gsa3
Copy link

gsa3 commented Feb 17, 2023

Hello,
while runing perl vcf2freq.pl, I encountered genotype format and looked at the code to modify it for the genotype format GT:DP:AD:GQ:PL:RNC. Could you please help wiht modifying the script for this format.
Thank you,
Shad

die("Your genotype format is not "GT:PL:AD". Looks like you used a different pipeline to generate the vcf file? You can modifiy this script if possible to support your format. Otherwise please follow the pipline given at https://github.com/USDA-ARS-GBRU/QTLsurge") unless $format eq "GT:PL:AD";
I have the following
GT:DP:AD:GQ:PL:RNC

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