[ensembl-dev] Add "Format/Qual /Filter / Info" fields from VCF in tabulated ouput of VEP

Will McLaren wm2 at ebi.ac.uk
Fri Jan 15 14:18:43 GMT 2016


Hello,

On 15 January 2016 at 14:00, Jean-Philippe Villemin <jpvillemin at gmail.com>
wrote:

> Hi,
>
> Question is in the title. I 'm using vep version 83.
>
> 1- Is this possible to add Format / Qual / Filter / Info  from VCF  in
> tabulated output of VEP ?
>

No. You may use VCF format output (--vcf) to preserve those fields from
your input VCF.


> ​2 - I noticed that TSL and APPRIS are always empty ... Why ?​ Is this a
> bug or misconfiguration ?
>

These fields are available only for Ensembl transcript sets and (in human)
the GRCh38 assembly.

Our GRCh37 gene sets were frozen at Ensembl release 75, which came before
these fields were added to our databases.

Regards

Will McLaren
Ensembl Variation


>
> ​Thanks guys !​
>
>
> ​My bash script is actually doing this : ​
>
>
> read -r -d '' VEP_PARAMETERS_TAB << EOM
> -i ${INPUT_PATH}${SAMPLE_FILE}
> -o ${OUTPUT_PATH}${SAMPLE_FILE}.vep.txt
> --verbose
> --no_progress
> --cache
> --merged
> --offline
> --fork 6
> --no_stats
> --buffer_size 10000
> --dir_plugins ${VEP_PLUGINS_DIR}
> --plugin dbscSNV,${DBSCSNV_PATH}
> --plugin MaxEntScan,${MAXENTSCAN_DIR}
> --fasta ${FASTA_PATH}
> --assembly ${VEP_DB_VERSION}
> --dir_cache ${VEP_DB_PATH}
> --no_escape
> --force_overwrite
> --everything
> --fields
> Location,SYMBOL,Gene,Allele,HGVSc,HGVSp,VARIANT_CLASS,Uploaded_variation,INTRON,EXON,Feature,CANONICAL,Consequence,IMPACT,CLIN_SIG,SIFT,PolyPhen,ada_score,rf_score,MaxEntScan_alt,MaxEntScan_diff,MaxEntScan_ref,APPRIS,
> ​TSL
> EOM
>
>       ${PERL_5_22} ${VEP}variant_effect_predictor.pl $VEP_PARAMETERS_TAB;
>
> --
> *Jean-Philippe Villemin   *- Bioinformatics, Software Engineer -
>
> IURC (Institut Universitaire de Recherche Clinique)
> 641 avenue du Doyen Gaston Giraud
> 34093 Montpellier Cedex 5, France
>
> *jpvillemin at gmail.com <jpvillemin at gmail.com>*
>
>
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