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

[Nikolas Pontikos]

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.