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.
Combine phased calls from Mutect2
Hello, is there a way to have Mutect2 emit multi-nucleotide variants instead of multiple adjacent SNVs?
For example, consider this variant:
Mutect will call the G/T SNP in position 2 as one line, and the G/C SNP at position 3 as another line. Then the fact that they are part of the same haplotype is indicated by the phasing information in the info column of the vcf.
I would prefer to have it call a multiple nucleotide variant: REF GG and ALT TC.
Can I get Mutect to do this? Or is there any post-processing tool you can recommend?
The reason for preferring MNVs instead of SNVs is that I am using ensembl-VEP to predict the protein consequences of the variants. In that case it's quite important to represent the actual haplotypes instead of stepping through variant sites one-by-one.