Closed PengZhangJHU closed 1 year ago
Hi @PengZhangJHU
Is the cnvs.gr
parameter overlapping the variants from the VCF? Remember that "only those variants in regions affected by CNVs will be loaded".
Also, in order to reproduce the issue, Could you please provide a fake VCF and a CNV file? Thanks :)
Thanks for your comments. I just realized the sample names are slightly different between the VCF and CNV file. It works now after I made the sample name consistent.
Hi
I was able to run loadVCFs() but it seems that no actual contents from VCF being loaded, as it shows '0 ranges and 8 metadata columns', whereas it worked well with CNVfilteR provided VCF. I don't see any obvious differences from the two VCFs. Any suggestions how to make it work? thank you!
experiment sample
Example vcfs provided by CNVfilteR with 13 ranges