As of yet, the old .writeCandidateVCFs function (see in history) didn't work because it only takes VCF objects (which can be created from VRanges objects), but we work with a GRanges object from the VEP step on. Thus, we can't write a VCF output file using that function.
Two ideas to make output VCFs possible:
Parse row names from GRanges to get the ref column needed to convert GRanges to VRanges
Output a VCF object from ensemblVEP. This would require refactoring the functions that follow (filtering, scoring, and ranking) to work with a VCF object rather than GRanges.
As of yet, the old
.writeCandidateVCFsfunction (see in history) didn't work because it only takes VCF objects (which can be created from VRanges objects), but we work with a GRanges object from the VEP step on. Thus, we can't write a VCF output file using that function.Two ideas to make output VCFs possible:
refcolumn needed to convert GRanges to VRangesensemblVEP. This would require refactoring the functions that follow (filtering, scoring, and ranking) to work with a VCF object rather than GRanges.