Closed garrettjstevens closed 7 years ago
This is related to #68. I'll have a look at these next week.
can you give: https://github.com/brentp/vcfanno/releases/tag/v0.2.7-beta a try and let me know if it resolves your issue.
I've been watching the discussion on #68, and it looks like I'm having the same problem (header is now Number=A, but it's now missing the annotation for the second ALT). I also got some warnings in the STDERR, all like:
api.go:216: WARNING: got single value %!s(float64=15.300000190734863) for value with Number=A
See the attached tar.gz for an full, minimal working example: test.tar.gz
I agree this is a tricky problem, but I am just fine with only the first case you describe in #68 being supported.
Thanks
that warning is from the last version of vcfanno, not the beta, right?
let's continue this in #68 to keep it centralized.
When I annotate a VCF using another VCF as a source, for lines where there are multiple ALT alleles I get comma-separated values for each INFO ID, e.g. using CADD:
This is exactly what I want. In the header tag that vcfanno adds, however, it has this:
It seems like this should be "Number=A", according to the VCF specs:
I'm guessing it might just be copying this value from the source VCF (the source has "Number=1", probably because it expects all variants with multiple ALT alleles to be split into single lines). Is there a way to get vcfanno to change this value to "Number=A", since that's what it is in the newly annotated VCF?
Thanks