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More robustly handle sample names in indel VCF headers

Open julianhess opened this issue 4 years ago • 1 comments

The VCF spec demands that the samples' column names match entries in the header (e.g. if ##normal_sample=MY_NORMAL is present in the header, then the column for the normal should be named MY_NORMAL.)

Previously, deTiN would break on otherwise valid indel VCFs. This fixes that. As a bonus, the deTiN output should be easier to merge with the input VCF, since the VCF column names are preserved.

julianhess avatar Dec 22 '20 15:12 julianhess

I've confirmed this works with Strelka VCFs, both malformed and header fixed. Need to test on M2 and Sanger before merging.

julianhess avatar Dec 22 '20 20:12 julianhess