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VCF - Combining two columns into one column
I have a VCF file with multiple samples (multiple columns). There are replicate samples.
Essentially, I want to combine two columns into one. The GT:AD:DP:GQ:PL data would obviously have to be recalculated. (The two columns representing replicate samples are replaced by a single column that represents them both together). I have tried CombineVariants, but the two columns are not combined into one.
Is there a GATK tool to do this for a VCF? Or do I have to go all the way back and concatenate the replicate sample FASTQ files together before rerunning the GATK pipeline? Is there any other way to combine replicate samples into one at some point in time other than when concatenating their FASTQs?