Question: Beagle 4 & Beagle 3.3.2 [Java Error]
gravatar for kate.ignatius
2.8 years ago by
kate.ignatius0 wrote:


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?


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