[ensembl-dev] Reordered VCF file?

[Martin Pollard]

Hi,

I’m having a problem with a specific VCF file.  I have run it through the VEP perl script twice and for some reason it reorders the VCF file so that part of chromosome 9 ends up interleaved with chromosome 10 in the VCF file.  The strange thing being that it’s happened in exactly the same region in the file.

9       BEGIN-139307194
10	93528-38598955
9	139308932-141071552
10	38599101-END

Any suggestions?

Martin

Command used:
perl /nfs/users/nfs_m/mercury/src/ensembl-tools-release-75/scripts/variant_effect_predictor/variant_effect_predictor.pl -i all.vqsr.dbsnp.vcf.gz -o all.vqsr.dbsnp.vep2.vcf --vcf -cache -dir_cache /data/blastdb/Ensembl/vep

Version info:

# ENSEMBL VARIANT EFFECT PREDICTOR #
version 75

Linux bc-19-3-01 2.6.32-44-server #98-Ubuntu SMP Mon Sep 24 17:41:33 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux

Distributor ID:	Ubuntu
Description:	Ubuntu 12.04.2 LTS
Release:	12.04
Codename:	precise

This is perl 5, version 18, subversion 1 (v5.18.1) built for x86_64-linux-thread-multi

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