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getzlab / deTiN

DeTiN is designed to measure tumor-in-normal contamination and improve somatic variant detection sensitivity when using a contaminated matched control.
BSD 3-Clause "New" or "Revised" License
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More robustly handle sample names in indel VCF headers #32

Open julianhess opened 3 years ago

julianhess commented 3 years ago

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 commented 3 years ago

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