Entering edit mode
3.0 years ago
rugarem
•
0
Hi everyone,
Just wanted to ask if anyone can help me locate the .vcf.stats
file supposedly made by Mutect2 along with the .vcf.
I've called my variants using Mutect2 on a cluster, got the vcf but no vcf.stats file. I need that file to filter using FilterMutectCalls. I've tried: find /users/username/ -name "*.vcf.stats"
and nothing. The information on the GATK webpage on this issue is no help at all.
I can't seem to specify where the vcf.stats file is dumped by Mutect2 either.
Anyone else run into this problem calling variants on a cluster and resolved it? Much appreciated in advance!
R
Please give us your exact Mutect2 command.
The Mutect2 command as requested below!
Your output directory is under
/ph-users/
. Why are you looking for the stats file under/users/
?Hello rugarem
Why did you delete this post?