local ancestry for each input snp

slowkoni / rfmix

RFMIX - Local Ancestry and Admixture Inference Version 2

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local ancestry for each input snp #12

Open complexgenome opened 5 years ago

complexgenome commented 5 years ago

Hello,

My input file has 21K snps on CHR 21 for a three-way admixed population. I phase my input data and follow steps necessary before running RFmix V2. However, my output in .msp.tsv file contains only 800 SNPs; similarly .fb.tsv output too.

If I tinker with -c <# of SNPs>option, this also doesn't help with desired output (ancestry per input SNP). How do I achieve desired result?

I think RFmix v1 generated ancestry result per input snp. Thanks!

guidebortoli commented 3 years ago

Hi @sariya... I see they never answered your question. Have you figured it out how to get the local ancestry for each SNP instead of window sizes (that is the .msp.tsv output)?

Thanks

complexgenome commented 3 years ago

@guidebortoli sorry, could not get it working.