Add sample number/name column to VEP result

Question

[Abdul Rafay Khan]

Is there any way to add a sample number/name column to VEP result file when the merge vcf file of multiple samples is annotated with VEP.

Answer 1

[Emily]

If you get your output as VCF, it will preserve all the columns of your VCF, just adding the VEP annotation to the INFO column. This means that if you have any genotype columns, it will keep them. If you want to get the data out in another format, then maybe consider adding that information into the ID column in your input, so it can saying something like rs334_sample1.