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

Hi,

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:

http://faculty.washington.edu/browning/beagle/beagle.29Sep14.pdf

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:

http://faculty.washington.edu/browning/beagle_utilities/utilities.html#vcf2beagle

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?

Thanks!

ADD COMMENTlink modified 2.7 years ago • written 2.8 years ago by kate.ignatius0
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