Marghoob Mohiyuddin

Hi Wenxian, Which version of VarSim are you using? The most recent version (v0.5.2)[https://github.com/bioinform/varsim/releases/tag/v0.5.2] should support single-ended reads in samcompare. Please try to run with the latest version and let...

@haoziyeung Could you please attach your log directory as a tar-gzipped archive and we will have a look. It looks like one of the processes failed for some reason and...

@MaestSi could you please provide the complete log from BreakSeq output?

The breakpoints library is maintained by Prof. Gerstein's lab so I am not sure if they have any plans to update the breakpoints library for hg38.

@jiangyuanluo and @countdigi there is no official release of an hg38 breakpoint library from Prof. Gerstein's lab. I can provide you a lifted over breakpoint library from b37. Would this...

Hi @countdigi and @jiangyuanluo , I am attaching a GFF file for the breakpoint library which was generated after lifting over to hg38. Note that this only includes deletions since...

@weikai320722 , the high-quality SVs would have PASS in the FILTER column in the VCF.

Did you check that spades.py is executable and runnable by you? Apologies for the delay since I am traveling currently.

Thanks, Amanda. Please let me know if the solution worked so that I can fix/close this bug. Best Marghoob

Thanks, I am glad it worked for you!