Look into source code of BEAGLE 4.1

[szhan]

I should know a bit better the nitty-gritty details of the LS HMM implementation of BEAGLE 4.1. The source code (Java) of BEAGLE 4.1 is not available (download link) when I checked, so I've emailed Brian Browning for a copy.

[szhan]

The broken link is now fixed.

[szhan]

In the BEAGLE 4.1 paper, it states that an allelic error rate of 1-e04 is used. This should reflects sequencing error in NGS data. And it should be much higher than the generational mutation rate in humans (in the order of magnitude of 1e-08). So, I'm going to try using the parameter combination of r = 1e-08 and m = 1e-04 in the next run to see if I get better imputation results.

[szhan]

This thread is better moved to https://github.com/szhan/onekg_analysis.