Add INFO tag to one VCF if record present in a second VCF

Question

[Sean Davis]

I have a VCF file to which I would like to add an INFO flag for every record that is present in another (LARGE) VCF file. There are a number of tools to do filtering and another set of tools that will merge INFO fields from one VCF to another, but this isn't exactly what I need (though the latter could be adapted, I suppose).

The use case is that I am trying to do a simple panel-of-normals filter to a set of somatic variants. Should be simple, I know!

Answer 1

[Pierre Lindenbaum]

I wrote a tool like this https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/vcfvcf/VcfVcf.java but it's undocumented and I should update this old pre-htsjdk code.

The compilation should be:

ant vcfvcf

It works with a tabix indexed file. A usage would be:

java  -jar `dist/vcfvcf.jar` -H

java -jar  dist/vcfvcf.jar ACF=CONFLICTALT  INFO=TAG1 INFO=TAG2 \
  TABIX=tabix.vcf.gz \
  IN=in.vcf > out.vcf