Thanks for reporting this issue and workaround Ulf. I've committed a fix that 
addresses this issue by only includeing the -split option for BED/GFF/GTF 
datasets and not VCF:

https://bitbucket.org/galaxy/galaxy-central/commits/b8d8f81bed872e58b4691643de8a08fa41662e71

Best,
J.

On Sep 12, 2013, at 6:45 AM, Ulf Schaefer wrote:

> Dear Jeremy
> 
> Thank you for your reply and sorry for not being clear. In short I 
> solved the problem. Below is some info, in case this is useful for 
> someone else.
> 
> Thanks for your help
> 
> The situation was:
> 
> On Main:
> Visualisation of the SAM/BAM file -> OK
> Visualisation of the VCF file -> OK
> 
> On my local install:
> Visualisation of the SAM/BAM file -> OK
> Visualisation of the VCF file -> FAIL
> 
> The reason is that this command fails:
> 
> grep -v '^#' /data/database/files/000/dataset_596.dat | sort -k1,1 | 
> bedtools genomecov -bg -split -i stdin -g 
> /data/database/files/000/dataset_598.dat > temp.bg ; bedGraphToBigWig 
> temp.bg /data/database/files/000/dataset_598.dat 
> /data/database/files/000/dataset_609.dat
> 
> with "Input error: found interval with block-counts not matching 
> starts/sizes"
> 
> Where dataset_596.dat is my vcf and 
> /data/database/files/000/dataset_598.dat is my genome file.
> 
> This is produced by the bedtools genomecov bit of the command, which 
> appears to have some sort of problem with the vcf input in combination 
> with the -split option. The problem disappears with the installation of 
> the latest version of bedtools (v2.17.0), but if you are using the 
> version that you get from yum (v2.15.0) you run into this error.
> 
> Ulf
> 
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