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

[Jean-Philippe Villemin]

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

​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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