Annotation using TSV files (like CADD)

[Edoardo Giacopuzzi]

Hi,

I want to implement vcfanno in our workflow for VCF file annotations.

Following your examples to annotate using large files like CADD, I've noticed that it is possible to directly annotate using TSV files as annotations source. 

In your config example, you specified the CADD TSV file and then 'columns=[4, 5]'.

However, I have a doubt on the use of TSV files. Can vcfanno consider also REF and ALT bases (indicated in columns 3 and 4 of the standard CADD file for example)? Is some special configuration needed for this?

Or the annotation is based only on genomic positions when a TSV file is used as an annotation source?

Thanks for your help!

Edoardo

[Brent Pedersen]

Hi, if your file has a header with "reference" or "ref" and
"alternate" or "alt" (case-insensitive), then vcfanno will do allele
matching on a tsv.
-Brent

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