[ensembl-dev] VEP, all columns from dbNSFP are empty

Jean-Philippe Villemin jpvillemin at gmail.com
Tue Jan 12 15:34:23 GMT 2016


Hi,

I'm working with VEP 83 under MacOsX.

I meet some troubles with VEP using dbNSFP 2.9. (for hg19, I downloaded
from this page http://snpeff.sourceforge.net/SnpSift.html#dbNSFP)
I'm using MaxtEnScan and dbscSNV plugins too. Here, everything is ok.

My script makes a vcf and txt ouput. For both of them, data from dbNSFP are
empty.
The column names from dbNSFP are present in the ouputs but with no values
inside the respective columns.
No errors are output when vep is running on dbNSFP 2.9.

This globally how I use VEP to get txt output:

-i ${INPUT_PATH}${SAMPLE_FILE}
-o ${OUTPUT_PATH}${SAMPLE_FILE}.vep.txt
--verbose
--no_progress
--cache
--refseq
--offline
--fork 6
--no_stats
--buffer_size 10000
--dir_plugins ${VEP_PLUGINS_DIR}
--plugin
dbNSFP,${DBNSFP_PATH_29},PROVEAN_score,SIFT_score,ExAC_NFE_AC,genename
--plugin dbscSNV,${DBSCSNV_PATH}
--plugin MaxEntScan,${MAXENTSCAN_DIR}
--fasta ${FASTA_PATH}
--assembly ${VEP_DB_VERSION}
--dir_cache ${VEP_DB_PATH}
--fields
Uploaded_variation,Allele,Location,Consequence,IMPACT,PROVEAN_score,SIFT_score,ExAC_NFE_AC,SYMBOL,genename,Extra,MaxEntScan_ref,MaxEntScan_alt,MaxEntScan_diff,ada_score,rf_score
--no_escape
--force_overwrite

I check with tabix too if my dbNSFP29.gz had the values for gename for
example.

So , with :

*tabix dbNSFP29.gz 1:109446750-109446750*

I retrieve "GPSM2" for the genename column.

But when I look to the Vep outputs (vcf or txt file) in "Extra Column" or
"genename Column", there is no value found.

Is this a bug or Am I doing something wrong ?

I join 4 files in a zip :

- COMMAND_VEP.txt : how I execute VEP.
- LOG_VEP.txt : VEP output
- OUTPUT_TABIX.txt : tabix output on my dbNSFP29.gz for
1:109446750-109446750
- SU4184.final.vcf.vep & SU4184.final.vcf.vep.txt : output from vep.

Thanks for you help,


-- 
*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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