If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.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.
Allele depth difference between mutect VCF and IGV
Dear Mutect team,
I usually use Mutect for calling somatic mutations. I faced problem with depth in variant position.
We use both paired (tumor- matched normal) and tumor only analysis. For instance, Mutect called somatic mutations as follows:
7 55259445 . C T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:62,9:24:71:0.127:2 0:0,0:.:0:0.00:0
7 55259446 . A T . PASS SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0/1:63,7:26:70:0.100:2 0:0,0:.:0:0.00:0
These two positions have approximately 70x for total reads and 10% variant allele frequencies in VCF file
However, the total depth and variant allele depth in those position were 200x and 100x (50%) in IGV.
Please let me know why VCF present quite less read depth than IGV. Are there any reads filtering steps for calling variants?
I have one more question. If there are overlapped reads that are originated from insert size ( e.g) 250bp - insert size, 150 bp * 2 - sequencing read), how does Mutect treat the reads?