I am having all kinds of trouble with loading files from 1000 Genomes into Haploview. This seems to be specific to the new update (v5 just updated Sept 17 2014) of the Phase 3 "20130502" release. I can load a .ped downloaded Sept 14 2014 just fine. If I generate the same .ped today (Sept 18 2014) with the same genomic coordinates and from the same population from the 1000 Genomes VCF to PED converter, I get a fairly consistent error message even if I try different segments of the chromosome I am interested in:
"file input error on line [x], marker [y]. For any marker, an individual's genotype must be only letter or only numbers."
where x is usually somewhere in the first ten lines, and y is the last marker in the sample.
I have checked the files manually and there no not seem to be any non- ACGT characters, spaces at the end of the line before the line break, or anything unusual about the file.
Advice would be greatly appreciated.