If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
GATK 22.214.171.124 Mutect2 doesn't emit a real variant
Hello GATK team,
I have been trying the brand new Mutect2 v126.96.36.199 on ctDNA samples with high coverage. I noticed one case where Mutect2 v188.8.131.52 detected a variant, but the new version didn't even emit the mismatch.
Here is the original command I used:
gatk Mutect2 -R reference.fasta -I normal.bam \ -O variants.vcf.gz --germline-resource gnomadhg19.vcf.gz \ --panel-of-normals pon.vcf.gz -L targets.interval_list \ -ip 300 -normal normalSample -I tumor1.bam \ -I tumor2.bam -I tumor3.bam -I tumor4.bam
When I realized the missing variant, I reran Mutect2 with the following additional parameters, but that didn't help.
--force-active true --tumor-lod-to-emit 0 --initial-tumor-lod 0
Here is an IGV snapshot of the variant (it exists in only one tumor sample: Ref: 820, Alt: 29, N: 2)
The reads in the upper part are from the original bam and in the lower part from the bam file emitted by Mutect2
Thank you for your help