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Error With bwakit Alignments #61

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DarioS opened this issue May 6, 2020 · 0 comments
Open

Error With bwakit Alignments #61

DarioS opened this issue May 6, 2020 · 0 comments

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@DarioS
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DarioS commented May 6, 2020

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

It should not fail in this case.
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@DarioS