I'm interested in identifying somatic mutations (using matched samples) both in the non-HLA and HLA regions.
For the HLA regions, one approach I've used, was to utilize known HLA-typing information about my samples to align to the specific HLA-alleles and then adapting the Mutect2 workflow. My post https://gatk.broadinstitute.org/hc/en-us/community/posts/4417333390619-ApplyBQSR-for-somatic-mutation-detection-in-HLA-regions referred to this approach.
Now, I would instead like to try a different approach, leveraging hg38 and the alt-aware alignments. I found the following (non-production) workflow: https://gatk.broadinstitute.org/hc/en-us/articles/360037498992#6, which has indication on how to call variants on HLA using alt-contigs. I'm wondering if anybody can point me to or can share an analogous workflow, but specific to somatic mutation calls using paired (tumor/normal) samples, aimed at HLA somatic mutation detection.
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