vcfanno

Hi Sugi, vcfanno can only annotate by position, not by gene id. Your "GnomAD constraint scores

Hi Sugi, for gene annotation, it's best to use a tool like snpEff or bcftools CSQ as those will

Hi, I'm testing vcfanno using the conf file here, as recommended in the vcf2db documentation.

Hi, if your file has a header with "reference" or "ref" and "alternate"

I agree this could be supported better, but you can probably do: [[postannotation]] name="gene

Hi Brent, Sorry about that. I used 'shuf' to randomly select rows from the original file but

Hi Phil, this isn't possible right now. I guess I could expand user vars in file paths, but they

Hi Bogdan, I'm not sure what your question is. In this case, if the POS and the END (from the

Thanks again Brent, you're right, those lines were from the dbSNP, just warnings though. The DB

Thanks a lot for the quick and detailed response Brent! I was able to get rid of that error message,

Awesome, thanks a lot! All the best, Laure > On Dec 15, 2017, at 10:28 PM, Brent Pedersen <

Hi, Thanks for this - I'll use bcftools in that case, Sirisha On Friday, August 11, 2017 at 1:58:

On Wed, May 24, 2017 at 1:00 PM, Daniel Cook <danie...@gmail.com> wrote: > Is it possible

On Tuesday, 11 April 2017 11:39:37 UTC-6, Joel Lafond Lapalme wrote: Hi, Is it possible with vcfanno

Well, it won't do all of that for you but if you annotated with a bed or GTF file of genes and --

Hi All, I just made a big release of vcfanno. Most importantly, it has proper support for

Oh, I see. Yes. You'll use fields=["ID"] to grab the ID field from the annotation file.

Hi, I missed this when you originally posted. If you use vcfanno with the -ends argument, it will

I just released a new version of vcfanno. It contains usability changes and bug fixes for annotating

Thanks for the feedback. I've pushed these changes to master so that: when op=self, pull Number

I just posted binaries for the 0.0.10 release here: https://github.com/brentp/vcfanno/releases this

I have just released a new version on github that has performance improvements and bug fixes and some

vcfanno 0.0.9 has just been released here: https://github.com/brentp/vcfanno/releases Along with a