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bioinform / breakseq2

BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of structural variants
BSD 2-Clause "Simplified" License
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error breakpoint file #14

Closed guillaume-rs closed 6 years ago

guillaume-rs commented 7 years ago

Hello,

I'm trying to use Breakseq2 to detect structural variants on my data.

Unfortunately I'm not working on human data, and then, cannot use the breakpoint library given in parameters. ( http://bioinform.github.io/breakseq2/)

When I try to use the programme without this parameter I have the following message :

" Atleast one of the breakpoint FASTA or GFF must be specified ", and it doesn't work either with an empty file.

Would you know a way of using Breakseq2 without giving a breakpoint library file?

Thanks

Guillaume

marghoob commented 7 years ago

Hi @guillaume-rs the BreakSeq2 algorithm is based on matching reads to known junction sequences (corresponding to known SVs). So, without a breakpoint library, BreakSeq2 cannot work.