Hello GATK community,
This post is more of a question about LiftOver behaviour than a troubleshooting one.
I want to lift over archaic human genomes from hg19 to hg38. I cannot understand how LiftOver will deal with multiallelic positions (when archaic human ALT is different from modern human ALT).
Option 1) is LiftOver only checking position and strand from the chain file and, as a result, lift over any position with ALT different from the hg19 or hg38 ALT?
Option 2) does LiftOver use an extra step which checks whether REF and ALT from the genome to be lifted correspond to REF and ALT either in hg19 or hg38? In this case, rejecting any multiallelic site in the archaic human genome, and increasing resemblance with the modern human reference genome.
I hope this makes sense. Please, if someone better understands LiftOver I would appreciate any insight.
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