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.
Haplotype phasing somatic mutations from MuTect2 using read-backed phasing and parental data
To whom it may concern,
I have both normal and tumour sample and I also have the parental data (both mother and father) for the patient sample. I hope to first haplotype phase the SNP and INDELs from the haplotype caller using PhaseByTransmission. Thereafter, I wanted to haplotype phase the somatic mutations from MuTect2 using Read-Backed Phasing.
I wanted to ask whether the Read-Backed Phasing method will consider both the SNP and INDEL encompassed within the read and whether it will also consider the information from PhaseByTransmission when haplotype phasing the somatic mutations.