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!
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written
by
JourneyToAbyss
1 answer
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
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