Considering "NON-REF" as a literal during merge

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Considering "NON-REF" as a literal during merge #819

Open arkopravoghosh opened 6 years ago

arkopravoghosh commented 6 years ago

When trying to merge VCF and GVCF files using BCF files, "NON-REF" under the ALT field is being considered as a literal instead of a symbolic reference. VCF tools list all "NON-REF" fields in the end and and thus it is easy to filter them out.

I've looked at the source code for the BCF tools and tried to make an alteration to the code but I haven't been able to do so successfully.

Any suggestions on how to rectify this problem?

Thank you!

pd3 commented 6 years ago

Can you give an example of such a VCF? The string "NON-REF" should not appear in the ALT column, please check the VCF specification.