I have RNA-seq data from ~30 related mice (C57Bl/6 strain). I am not studying cancer. Instead I have RNA from a specific brain region, plus RNA that is enriched for a specific cell type in this region.
I want to identify the somatic mutations present in each sample.
I have followed the Best Practices workflow for preprocessing RNA seq data, up to the production of base-recalibrated BAM files. I have run haplotypecaller on all samples to identify germline variants to exclude from a somatic analysis. I will perform hard filtering on these.
To find somatic variants, I came across this workflow for comparing two samples. Is this the right route to go down for such an analysis? I am confused as to how to structure my comparisons to get somatic mutation information for every sample.
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