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 > ; bedGraphToBigWig /data/database/files/000/dataset_598.dat 

with "Input error: found interval with block-counts not matching 

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.


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