[ensembl-dev] Filtering plugins

[Will McLaren]

Hi Konrad,

This is a bug in the output handler for VCF files.

I've fixed it in the ensembl-variation module on release/75. Update your
API checkout or rerun INSTALL.pl to pick up the fix.

Thanks for your help finding these!

Regards

Will


On 20 May 2014 07:43, Konrad Karczewski <konradk at broadinstitute.org> wrote:

> Hello again,
>
> I've noticed some odd behavior when using the filtering capability of
> plugins. I ran the RankFilter plugin with at minimum intron_variant's
> (--plugin RankFilter,intron_variant) and noticed that instead of not
> printing the consequence it prints a set of blank fields. In the extreme
> case, I get a line like:
>
>
> CSQ=|||||||||||||||,|||||||||||||||,|||||||||||||||,|||||||||||||||,|||||||||||||||,|||||||||||||||,|||||||||||||||,|||||||||||||||
>
> Is this expected behavior or am I missing something: shouldn't these be
> removed completely?
>
> Full call: perl variant_effect_predictor.pl -i input.vcf.gz -o output.vcf
> --cache --compress "gunzip -c" --vcf --force_overwrite --offline --fork 4
> --fasta
> ~/.vep/homo_sapiens/75/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa
> --plugin LoF --plugin RankFilter,intron_variant
>
> Thanks!
> -Konrad
>
>
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