Could you please provide a breakpoint library for HG 38?

[jiangyuanluo]

Or maybe how to convert a breakpoint library from other hg to hg 38?

[countdigi]

+1 for this request - we are aligning based on a GRCh38 human reference genome (https://genome.sph.umich.edu/wiki/Vt#GRCh38) and are interested in a breakpoint library for HG 38 as well. Thank you!

[marghoob]

@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 work for you guys?

[jiangyuanluo]

Hi @marghoob. This will work for me. Thanks!

[countdigi]

@marghoob - Yes - I am working with Dr. Parikh (you have correspondence with him) so either of us is fine to get the library too (just so you are not duplicating your effort :-). Thanks again! Kevin

[marghoob]

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 insertion liftover would require more checks and also need to update the INS file. In order to use the GFF, simply use the --bplib_gff <BPLIB.GFF> option. You do not need to specify the breakpoint library as a FASTA, but you need to specify the reference FASTA. If you need insertions (there are only a handful, ~400 insertions in the breakpoint library), I can help you with the liftover process there.
bplib.hg38.gff.gz. Please give it a try and let me know if there are any problems.

[countdigi]

Downloaded it - for now we will just concentrate on the DELs - thank you!

[Rohit-Satyam]

Hi was there any progress in incorporating Insertions in the above .gff file?