Hi everyone,

I have a custom tab delimited annotation file that I used to annotate a VCF file using bcftools annotate. It worked just fine but the only problem is that if there are multiple hits on a particular position, only the first information is carried into the VCF file. Here's an example:

This is an example of my annotation file:

#CHROM  FROM    TO  TRAIT
chr3    100001  100010  Disease A
chr3    100005  100005  Disease B
chr3    100005  100005  Disease C

And here's an example of my VCF file:

#CHROM  POS ID  REF ALT
chr3    100005  .   A   T

Annotating the VCF file produce:

#CHROM  POS ID  REF ALT INFO
chr3    100005  .   A   T   Disease A

As you can see, only the first information is carried forward. My ideal output is:

#CHROM  POS ID  REF ALT INFO
chr3    100005  .   A   T   Disease A
chr3    100005  .   A   T   Disease B
chr3    100005  .   A   T   Disease C

Or:

 #CHROM POS ID  REF ALT INFO
 chr3   100005  .   A   T   Disease A | Disease B | Disease C

Is there an option in bcftools annotate that would allow me to get such output? If there is an alternative tool, do recommend as well. Cheers.