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.

Sign up for GitHub

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

Jump to bottom

AF ignored - GATK4 MuTect2 case-change #12

Closed
ibwoo opened this issue Apr 26, 2018 · 1 comment
Closed

AF ignored - GATK4 MuTect2 case-change #12

ibwoo opened this issue Apr 26, 2018 · 1 comment

Comments

@ibwoo
Copy link

ibwoo commented Apr 26, 2018

MuPeXI/MuPeXI.py

Line 417 in 4430334

if 'ID=MuTect2,' in line:

MuPeXI does not recognise GATK4's new Mutect2-generated VCF files due to the case-change of the program name (MuTect2 -> Mutect2). The VCF files still report AF in the same way.

Case-change explained here:
https://gatkforums.broadinstitute.org/gatk/discussion/10911/differences-between-gatk3-mutect2-and-gatk4-mutect2
@ambj
Copy link
Owner

ambj commented Apr 30, 2018

Thank you for noticing this and informing me.
The bug have now been fixed on the master branch

Best,
/AM

@ambj ambj closed this as completed Apr 30, 2018
@ambj ambj mentioned this issue May 2, 2018
Closed
@ibwoo ibwoo mentioned this issue Jan 24, 2019
Open
@kobejamescurry kobejamescurry mentioned this issue Mar 5, 2019
Open
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
2 participants
@ambj @ibwoo