Open vindex10 opened 3 years ago
hi, you can fix this by changing your exac.vcf.gz to not have the FORMAT field. If the FORMAT field is present, it expects to have sample information.
Do you think it could be weakened easily? Because according to the VCF standard there can be "arbitrary number of sample IDs", I read it as including 0 :) https://samtools.github.io/hts-specs/VCFv4.3.pdf#subsection.1.5
It is of course a cosmetic change, but would be nice to have, if it doesn't affect efficiency and straightforward to implement.
Thank you for the neat and fast VCFAnno :)
Hi @brentp,
A minor follow-up on this one. When I run vcfanno (v0.3.3) on a VCF with no FORMAT
or sample genotypes (only the eight mandatory columns), the annotated VCF produced by vcfanno gives me the following header:
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT
I guess the FORMAT column should be skipped here?
best, Sigve
Just noticed https://github.com/brentp/vcfanno/issues/123, so this behaviour is already reported. Sorry for the duplication.
@sigven , I'll add this back into the queue and try to get a fix out.
Hello! I've discovered an error in a somewhat specific usecase. Here is the error:
Please find files in the attachment.
example.tar.gz
When annotating from VCF, tt looks like VCFAnno expects for the annotator source at least one sample in the VCF if FORMAT field is provided.
Thank you!