We used bwakit which does alignment to hg38 with alternative contigs and the HLA alleles. mut.to.sigs.output has an error if the VCF file has variants on such contigs.
mutationMatrix <- mut.to.sigs.input(allMutations, bsg = Hsapiens)
Error in .getOneSeqFromBSgenomeMultipleSequences(x, names[i], start[i], :
sequence HLA-A*01:01:01:02N not found
We used bwakit which does alignment to hg38 with alternative contigs and the HLA alleles.
mut.to.sigs.outputhas an error if the VCF file has variants on such contigs.It should not fail in this case.