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Published 20 hours ago • verified publisher icon fritzsedlazeck

BEDPE output

Open mike-molnar opened this issue 2 years ago • 4 comments

Hi, I'm testing out Sniffles2, and in the --help it says for output in BEDPE to use -b or --bedpe but it stops and reports that they are unrecognized arguments. Will there be an option for BEDPE output with Sniffles2?

Thanks, Mike

mike-molnar avatar Apr 05 '22 16:04 mike-molnar

Hey Mike, I would need to check again, but Snfifles2 doesn't have bedpe support as far as I know. Moritz will know for sure. thanks Fritz

fritzsedlazeck avatar Apr 05 '22 16:04 fritzsedlazeck

Okay, thanks Fritz. I prefer BEDPE because I use bedtools a lot.

mike-molnar avatar Apr 05 '22 17:04 mike-molnar

I see. You can use it with VCF files, but I don't know how well bedtools take into account the END tag.

The "problem" is that VCF files is the main adopted format I think... We can ask Moritz to provide a printer for this format.

I do have also some conversion tools for VCF -> Bedpe but I would need to test them again..

Thanks Fritz

fritzsedlazeck avatar Apr 05 '22 17:04 fritzsedlazeck

Hi Mike,

currently Sniffles2 supports VCF & VCF.gz output only - I just added BEDPE output to the planned features list. Before this is implement, using a VCF->BEDPE conversion tool is also what I'd suggest in the meantime.

Thanks, Moritz

smolkmo avatar Apr 05 '22 18:04 smolkmo