Support the latest version of beagle
Reflect changes in bcftools som: the number of training sites is not required anymore
Initial commit of the shapeit pipeline and its helper script
Deleted
Classify both FILTER="PASS" and "." sites, not just "PASS"; Changed the output plot, now using number of sites on x-axis instead of sensitivity, which was too coarse; When testing all combinations, do not forget about all annots included
Merge branch 'develop' of /software/vertres/git/origin/vr-codebase into develop