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enormandeau / snplift

Transfer coordinates across genomes
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Can snplift swap REF and ALT if reference allele was changed? #3

Closed bsb2014 closed 1 year ago

bsb2014 commented 1 year ago

Can snplift swap REF and ALT (including genotype) if reference allele was changed? thanks.

enormandeau commented 1 year ago

This is not a case that is treated by SNPLift. I suggest you swap the alleles and genotypes prior to using SNPLift to align to another genome.