slowkoni / rfmix

RFMIX - Local Ancestry and Admixture Inference Version 2
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Unable to handle the swap of REF/ALT allele? #42

Open eldronzhou opened 1 year ago

eldronzhou commented 1 year ago

Hi,

Does Rfmix2 check and handle the swap of REF/ALT allele between vcfTarget and reference panel? Based on my testing, it seems that Rfmix does not handle this and could lead to incorrect results.