[ensembl-dev] Reordered VCF file?

[Will McLaren]

Hi Martin,

Thanks for finding this - there was a bug in the sorting method.

I've pushed a fix to GitHub on the release/75 branch, are you able to
update your API checkout, or rerun INSTALL.pl to pick up the fixed API?

Regards

Will McLaren
Ensembl Variation


On 28 March 2014 13:55, Martin Pollard <mp15 at sanger.ac.uk> wrote:

> 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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