[ensembl-dev] VEP -pick option

[Will McLaren]

Hi Yuan,

This seems to work for me, I get the following output for that line using
--pick:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
22      16287454        .       G       A       .       .
CSQ=A|ENSG00000198062|ENST00000343518|Transcript|synonymous_variant|484|432|144|P|ccC/ccT|||-1

Check that you are using API v75 and that everything is up to date.

I'd also check that there aren't any options that clash with --pick in your
config file, for example --most_severe or --per_gene

Regards

Will


On 21 May 2014 10:46, Yuan Chen <yuan at sanger.ac.uk> wrote:

> Hi Will,
>
> I am using VEP version 75 with -pick option, I am expecting to only get
> one consequence in output file, but it looks I am still getting multi
> consequences :
>
> 22      16287454        .       G       A       46.7    PASS
>  AC1=1;AC=1;AF1=0.0005889;AN=2014;DP4=3975,3745,7,2;DP=7968;FQ=46.7;HWE=1.000000;ICF=-0.00050;MDV=5;MQ=29;MSD=10;MSQ=33;PV0=0.18;PV1=0.025;PV2=1;PV3=1;PV4=0.18,0.025,1,1;QD=0.1006;SB=0.1983;VDB=0.0128;AA=.;CSQ=A|ENSG00000198062|ENST00000452800|Transcript|synonymous_variant&NMD_transcript_variant|264|264|88|P|ccC/ccT|||,A|ENSG00000198062|ENST00000343518|Transcript|synonymous_variant|484|432|144|P|ccC/ccT|||
>        GT:PL:DP:DV:SP:GQ:GL:PS 0/0:0,33,181:11:
>
> The command is :
>
> variant_effect_predictor.pl -i ShapeITphasedLCSamples_chr22.vcf.gz -o
> ShapeITphasedLCSamples_VEP_chr22.vcf -config vep_config_file -pick
>
> Is any way to check the option -pick is used in calculation?
>
> yuan
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