Links to programs, utilities and scripts:
IBDNE, BEAGLE (for phasing), Refined IBD (for IBD detection, including gapfilling), Beagle Utilities (for filtercolumns.jar), RFMix, python scripts and script for running RFMix (for adjust_npairs.py, filter_gapfilled_ibd_ancestry.py, rephasevit.py and run_rfmix).
Link to simulated data. This file has the sequence of commands that can be used to replicate the simulated data analysis, using these data and the above-linked scripts.
If you find problems with these commands/scripts, please contact Sharon Browning: firstname.lastname@example.org