[ensembl-dev] VEP -pick option

[Yuan Chen]

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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