Request for BEAGLE tutorial

Question

[akang]

Could someone please do a tutorial for BEAGLE(https://faculty.washington.edu/browning/beagle/beagle.html) imputation starting from plink ped and map files? It would be a great help to many including me, ofcourse.TIA!

[thakkarrajesh151]

hello I'm unable to install beagle in windows and also tried for Linux if someone could please do a tutorial for BEAGLE(https://faculty.washington.edu/browning/beagle/beagle.html) imputation starting from plink ped and map files or any other platform where I can get informative video ?

Answer 1

[Jason Chen]

BEAGLE is quite straightforward and usually just the one line, so the documentation should suffice. I think that the real question you have is how to convert from PLINK format to VCF format (which is the only thing the newest BEAGLE can accept). For that, you could write your own script, or convert to BEAGLE 3 format (using the newest PLINK, for example), and then use the BEAGLE Utilities scripts to convert from BEAGLE 3 format to VCF. I think that Mega2 can also do this conversion directly.

[akang]

Thanks Jason! I'll give it a try.