My phased file contains alleles called 0 and 1 which are defined in files beagle site provided (e.g. ALL.chr1.phase1_release_v3.20101123.filt.int), so I'm getting an error:
Illegal base [0] seen in the allele
Maybe I can replace the 0/1 to the actual alleles before running the BeagleOutputToVCF, but do you have any plan to implement that.
Thanks a lot in advance,
Hiroko Matsui