medaka icon indicating copy to clipboard operation
medaka copied to clipboard

Published 20 hours ago • verified publisher icon nanoporetech

variant calling for gbk files?

Open katefgit opened this issue 1 year ago • 1 comments

I just started using me medaka_haploid_variant to find SNP between ONT reads and HA. I can see that it doesn't work with gbk file (as for e.g. when working with breseq software and Illumina reads). Is this right? and is there an alternative?

katefgit avatar Sep 08 '22 13:09 katefgit

Medaka does not support gbk files as input, only fasta. If you wish to annotate the output VCF file you will need to use a standalone program dedicated to that task.

cjw85 avatar Sep 13 '22 10:09 cjw85