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Old 02-07-2017, 01:19 PM   #418
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

Originally Posted by Mat29 View Post
Thank you for developing BBMap. Could you please advise how to preprocess the output VCF to make it compatible with VCFAnnotator, SNPEff. I recieve "No gene feature" and "Chromososme is missing" errors on annotation. Tried Pilon also VCFs and errors persist.
Please ensure that your chromosome names do not have spaces in them. If they do, use the "trd" flag when mapping (trim read description), or for simplicity, just process the fasta initially like this: in=ref.fa out=fixed.fa trd

...then use fixed.fa for mapping and everything else.
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