Hello, I'm a new GATK user and am working on detecting somatic mutations both in non-HLA and HLA regions using Mutect2. For non-HLA mutation calls, I've followed the recommended pipeline both for preprocessing and for somatic mutation calling (in particular genome build b37 as for somatic mutation this is still the supported build).
I already have the HLA types for my samples. Thus, for the HLA-regions, I'm following an approach in the spirit of the Polysolver shell_call_hla_mutations_from_type but am trying to also account for the newer GATK software. I've aligned with Novoalign the original fastq files (which I also used for the non-HLA mutation calling pipeline) to the specific HLA-type sequences and have removed dups and used the Polysolver filters and "changing flags and mapping quality" script. At this point Polysolver would run mutect. I plan to run Mutect2 instead. But before running it, I wanted to ApplyBQSR to proceed in an analogous manner as done for the non-HLA. My question is: for the latter, is it appropriate to use the recalibratioin table previously computed for these samples in the standard pipeline for non-HLA mutation calling? It seems to me that it would be, but would appreciate feedback. Thanks.
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