local ancestry for each input snp

[complexgenome]

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]

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]

@guidebortoli sorry, could not get it working.