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slowkoni / rfmix

RFMIX - Local Ancestry and Admixture Inference Version 2
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whole genome level ancestry feature from version 1 missing #25

Open raqueldias opened 4 years ago

raqueldias commented 4 years ago

RFmix version 1 was able to calculate global ancestry proportions better than Admixture software, but it seems that this feature of global ancestry calculation per whole genome was removed in version 2, since only one single chromosome can be specified per run. I was wondering if there is a way to aggregate the global ancestry per chromosome into a global ancestry per genome level. What is the recommended approach to merge the rfmix2 results per chromosome and replicate the global ancestry like the result from rfmix v1?

d1eone commented 3 years ago

I am having the same issue. It would be nice to have a weighted average per subject/sample, where the weight is genomic size -- or something like that. In RFmix v2, are the per-chromosome estimates of ancestry weighted? Regardless, I don't think you can just take the mean of every chromosome, as each chromosome has different amount of genetic material.