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

**************************************************************************
The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE
**************************************************************************