ancestry_pipeline icon indicating copy to clipboard operation
ancestry_pipeline copied to clipboard

Published 20 hours ago • verified publisher icon armartin

rfmix2

Open mfazel opened this issue 1 year ago • 3 comments

Is it possible to use rfmix2 in this pipeline and/or its results as input for rfmix2plink. It would have been easier if there was a toy example for this pipeline. Thanks

mfazel avatar Jun 29 '23 20:06 mfazel

I am also trying to generate a karyogram plot sig RFmix v2 results. Has anyone had any luck with converting the RFmix outputs into bed files for plotting?

DavYang avatar Aug 03 '23 14:08 DavYang

I'm not sure how accurate that is and if by bed file you mean plink bed, but you can use ExtractTracts.py to convert rfmix2 results to vcf and then use them by plink. Hope this helps!

mfazel avatar Aug 03 '23 22:08 mfazel

Appreciate the tip. After the VCF files are generated, how did you generate the 2 .bed files? I see that the karyogram plot requires bed_a and bed_b. In my case, I have RFmix2 results for 5 ancestries, and therefore ExtractTracts.py generates 5 sets of VCF and txt files. Would appreciate any pointers on how you did the subsequent file conversions/what was used for the 2 bed files.

DavYang avatar Aug 08 '23 22:08 DavYang