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I have a VCF file produced by mapping reads from chimpanzee onto the human genome. I want to take this VCF and do a liftover to the chimpanzee genome using picardtools LiftoverVcf. However, when I do this, everything gets dumped in the 'rejected' folder and labeled "MismatchedRefAllele".
I understand why this would be a good feature when you are mapping to the same species, but is there anyway to change this behavior in the program? I tried setting the "LIFTOVER_MIN_MATCH" parameter to 0, but that doesn't seem to do anything.
One possibility is to switch the "REF" and "ALT" bases in the original VCF and ignore all positions that have an allele frequency of 100% (AF=1.000)--i.e. fixed differences between human and chimpanzee. However, I'd prefer not to mess with the file too much myself if possible.
I also tried liftovervariants from and earlier version of GATK (2.9), but it doesn't seem like it supports lifting over between species.
Any thoughts would be much appreciated!