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So today I have to compare two different vcf (from different pipelines, only one of them is from GATK) and when I tried to combine it with combineVariants, I had an error because the references doesn't match:
The provided variant file(s) have inconsistent references for the same position(s) at chr1:1724719, A* vs. G*
I know why it's happening, but I don't know if there is an option/tools to "fix" the vcf from the other pipeline.
That I want to do is take the VCF created with a "bad" reference and use a command or GATK option to "fix" it according with the correct reference fasta file.
Thanks for your help!