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kevlar-dev / kevlar

Reference-free variant discovery in large eukaryotic genomes
https://kevlar.readthedocs.io
MIT License
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VCF Parsing Issue #381

Open 17tranap opened 4 years ago

17tranap commented 4 years ago

I'm running some BCFTools operations on the VCF outputs of the Kevlar pipeline (from simlike).

It's a small issue, but the VCF syntax stumbles on the INFO lines:

INFO=<ID=IKMERS,Number=1,Type=Integer,Description="number of "interesting" (novel) k-mers spanning the variant alternate allele">

This is because there are quotes around "interesting", and it makes it so that this line cannot be parsed.

It is also missing the INFO fields for CALLCLASS and PART.

standage commented 4 years ago

Thanks for the report @17tranap! I'm not actively working on kevlar at the moment, so it may take me some time to get around to fixing this.