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Published 20 hours ago • verified publisher icon tseemann

Extract the genes with variants

Open SolayMane opened this issue 3 years ago • 2 comments

I have a question not an issue about Snippy. Could we extract the genes that are affected by snp/indels from the query genomes?

SolayMane avatar Oct 01 '20 15:10 SolayMane

Hi @SolayMane ,

Please use bedtools to extract the genes that are affected. You can get the names of the genes that are affected from the snps.tab file, you can get the coordinates from the reference genbank file.

schultzm avatar Oct 01 '20 23:10 schultzm

I want to extract the genes from the query sequences not from the reference. Thank you

SolayMane avatar Oct 02 '20 07:10 SolayMane