<div dir="ltr">Hi Yuan,<div><br></div><div>This seems to work for me, I get the following output for that line using --pick:</div><div><br></div><div><div>#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO</div><div>
22      16287454        .       G       A       .       .       CSQ=A|ENSG00000198062|ENST00000343518|Transcript|synonymous_variant|484|432|144|P|ccC/ccT|||-1</div></div><div><br></div><div>Check that you are using API v75 and that everything is up to date. </div>
<div><br></div><div>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</div><div><br></div><div>Regards</div><div><br></div><div>Will</div>
</div><div class="gmail_extra"><br><br><div class="gmail_quote">On 21 May 2014 10:46, Yuan Chen <span dir="ltr"><<a href="mailto:yuan@sanger.ac.uk" target="_blank">yuan@sanger.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Will,<br>
<br>
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 :<br>
<br>
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:<br>

<br>
The command is :<br>
<br>
<a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> -i ShapeITphasedLCSamples_chr22.vcf.gz -o ShapeITphasedLCSamples_VEP_chr22.vcf -config vep_config_file -pick<br>
<br>
Is any way to check the option -pick is used in calculation?<br>
<span class="HOEnZb"><font color="#888888"><br>
yuan</font></span><br>_______________________________________________<br>
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<br></blockquote></div><br></div>