Annotate with other field than 'INFO'

[Joel Lafond Lapalme]

Hi Bret, 

Can vcfanno annotate vcf fields other than fields that are in 'INFO' ?

Like if I have a database vcf with a field called 'XYZ_id' that I want to add to my vcf.

Thank you

Joël

[Joel Lafond Lapalme]

Sorry Brent ** I misspelled your name!

[Brent Pedersen]

Hi,
vcfanno can use BED, BAM, VCF to annotate; so if you can get your data
into one of those formats then you should be able to annotate easily.
If you wanted to support pulling from a database, you'd have to write
a fair bit of custom golang.
if you can describe in more detail what you are trying to do then
perhaps I can help more.
-Brent

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[Brent Pedersen]

Oh, I see.
Yes. You'll use fields=["ID"] to grab the ID field from the annotation
file. Currently, you can only set an entry in the INFO of the query
file with that.

In the pending release, you'll be able to set the ID of the query file
with the ID from the annotation file. That release will be out this
week or early next.


On Thu, Mar 16, 2017 at 9:01 AM, Joel Lafond Lapalme
<joel.lafo...@gmail.com> wrote:
> Sorry I was not clear. My 'database' is a vcf. I want to add the 'ID' field
> of that database vcf to another vcf as a custom field like XYZ_ID.
>
> Joël