[ensembl-dev] VEP: Output must be vcf (--vcf) to use --tabix

[Will McLaren]

Hi Nikolas,

--tab is supported only from VEP 84 onwards [1], though you can get a good
approximation of it using --fields [2] and listing the fields you want in
the output.

The problem is that --tab is getting interpreted as --tabix, hence the
error you're seeing.

Regards

Will McLaren
Ensembl Variation

[1] :
http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#history
[2] :
http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_fields


On 27 July 2016 at 10:15, Nikolas Pontikos <n.pontikos at ucl.ac.uk> wrote:

> Hi,
>
> I'm get this error message:
>
> Output must be vcf (--vcf) to use --tabix
>
> when running the command below:
>
> chr=22
> /share/apps/perl/bin/perl
> ensembl-tools-release-82/scripts/variant_effect_predictor/
> variant_effect_predictor.pl
> --port 3337 \
> --ASSEMBLY GRCh37 --fasta /SAN/vyplab/UKIRDC/reference/human_g1k_v37.fasta
> \
> --cache --dir_cache
> /cluster/project8/vyp/AdamLevine/software/ensembl//cache/ \
> --sift b --polyphen b --symbol --canonical --check_existing
> --check_alleles  \
> --fork 4 --maf_esp --gmaf --maf_1kg \
> --no_progress --quiet \
> --custom CADD/chr${chr}.vcf.gz,CADD,vcf,exact \
> --custom Kaviar-160204-Public/hg19/VEP_annotation.vcf.gz,Kaviar,vcf,exact \
> --plugin
> Condel,/cluster/project8/vyp/AdamLevine/software/ensembl//Plugins/config/Condel/config,b
> \
> --plugin Carol \
> --plugin GO \
> --no_stats \
> --hgvs \
> --plugin HGVSshift \
> --plugin SameCodon \
> --input_file ${output}_VEP/chr${chr}_for_VEP.vcf \
> --tab \
> --output_file STDOUT
>
> How shoould I change my command line parameters?
>
> Many Thanks,
>
> Nikolas.
>
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