Merge 1000 Genome gentotype AND genotype likelihood VCFs together

Question

[JourneyToAbyss]

Hello,

I would like to merge two VCFs together. However, these VCFs contain the same samples but different information. One VCF contain genotypes (e.g. field = GT) whereas the other VCF contain genotype likelihood probabilties (e.g. FIELD = GL).

I am doing this so I can liftover both VCFs together.

The original VCFs are encoded in b37. When lifting over with GATK LiftoverVcf, I find that 100% of all variants are "succesfully" lifted over. For some reason, GATK's LiftoverVcf ignores VCFs entirely of GL fields.

Alternatively, if someone knows of a way to liftover VCFs entirely of GL (no GTs)... that would also help.

Thank you!

Answer 1

[Giulio Genovese]

You can use BCFtools/liftover to liftover VCFs with GL information as it will properly handle the GL format field as well as other Number=G format fields when the reference allele changes and you can use BCFtools/annotate to merge VCFs with GTs and GLs