Open lconde-ucl opened 3 years ago
Hi, unfortunately this would be too difficult to support in vcfanno as it expects the entries in sorted order and looking at the other end of a BND would be a random lookup. As you note, it will work when there is a BND entry in the VCF for each end (which I think is what the vcf spec would dictate). perhaps you could write a post-processor that splits single entries into 2 BNDs before sending to vcfanno?
Hi Brent thanks for your quick reply. Yes, I can see how the sorting issue can make it difficult to implement. Splitting the BDNs is an easy workaround, so I'll do that. Thanks, Lucia
Hi,
I was wondering if it's possible to annotate both ends of a BND/TRA structural variant with vcfanno? From what I can see, it seems to annotate only one of the ends, but not the second.
For example, a BND variant in a VCF from Delly looks like this:
Using the config below (which simply annotates overlapping genes), vcfanno will correctly annotate the variant with the gene that overlaps the chr22:38186567 end, but it doesn't annotate the other breakpoint (chr6:35221592). However, for BNDs, you would want to know which genes are disrupted at both ends, not only one. Is there any option within vcfanno that allows both ends of the breakpoint to be annotated?
Please note that some SV callers like manta, output 2 entries per BND, for example:
so in that case, this is not a big issue as both ends will be annotated, but other SV callers like Delly and SURVIVOR only output one line per BND and therefore only one of the breakpoints ends up being annotated
Thanks Lucia