This is probably a fairly simple question... I recently downloaded Beagle 4 as it was fairly easier to use with vcf files. But to interpret - it wasn't easy as the documentation was only 7 pages compared to the other versions:
Therefore, to get more information out, I decided to use beagle 3.3.2 and converted my vcf to beagle format using vcf2beagle which seemed to work okay:
However, when I run Beagle 3.3.2 on the converted file I keep getting the following error:
Exception in thread "main" java.lang.IllegalArgumentException: Error: Marker positions must be nondecreasing: marker 2:10716
Just to note, "2:10716" is the first marker on chromosome 2. Thinking this might be a problem with marker names being chromosome and positions, I renamed these to the format: "Var-CHROM-POS but to no avail. I did specify lowmem=true, but that didn't help either. Both genotype and marker file is sorted by chromosome and position. Is there anything else that I'm missing here?