<div dir="ltr">Hi Eva,<div><br></div><div>You should get the data file and index from the line:</div><div><br></div><div><span style="color:rgb(0,0,0);font-family:Arial,SunSans-Regular,sans-serif;font-size:14px;background-color:rgb(149,204,236)">All possible SNVs of GRCh37/hg19   [ </span><a href="http://krishna.gs.washington.edu/download/CADD/v1.0/whole_genome_SNVs.tsv.gz" style="text-decoration:none;color:rgb(18,62,171);font-family:Arial,SunSans-Regular,sans-serif;font-size:14px;background-color:rgb(149,204,236)">file (79G)</a><span style="color:rgb(0,0,0);font-family:Arial,SunSans-Regular,sans-serif;font-size:14px;background-color:rgb(149,204,236)"> | </span><a href="http://krishna.gs.washington.edu/download/CADD/v1.0/whole_genome_SNVs.tsv.gz.tbi" style="text-decoration:none;color:rgb(18,62,171);font-family:Arial,SunSans-Regular,sans-serif;font-size:14px;background-color:rgb(149,204,236)">tabix index (2.7M)</a><span style="color:rgb(0,0,0);font-family:Arial,SunSans-Regular,sans-serif;font-size:14px;background-color:rgb(149,204,236)"> ]</span><br>
</div><div><span style="color:rgb(0,0,0);font-family:Arial,SunSans-Regular,sans-serif;font-size:14px;background-color:rgb(149,204,236)"><br></span></div><div>Regards</div><div><br>Will McLaren<br>Ensembl Variation<font color="#000000" face="Arial, SunSans-Regular, sans-serif"><span style="font-size:14px;background-color:rgb(149,204,236)"><br>
</span></font></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 3 July 2014 14:19, Eva Goncalves Serra <span dir="ltr"><<a href="mailto:egs@sanger.ac.uk" target="_blank">egs@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">



<div style="word-wrap:break-word;color:rgb(0,0,0);font-size:12px;font-family:Consolas,sans-serif">
<div>Hi, </div>
<div><br>
</div>
<div>I am a bit confused as to which file from <a href="http://cadd.gs.washington.edu/download" target="_blank">http://cadd.gs.washington.edu/download</a> I should download to use the plugin of CADD scores. </div>
<div><br>
</div>
<div>Any help would be appreciated. </div>
<div><br>
</div>
<div>Thanks!</div>
<div><br>
</div>
<div>Eva</div>
<div><br>
</div>
<span>
<div style="font-family:Calibri;font-size:11pt;text-align:left;color:black;BORDER-BOTTOM:medium none;BORDER-LEFT:medium none;PADDING-BOTTOM:0in;PADDING-LEFT:0in;PADDING-RIGHT:0in;BORDER-TOP:#b5c4df 1pt solid;BORDER-RIGHT:medium none;PADDING-TOP:3pt">

<span style="font-weight:bold">From: </span>Will McLaren <<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>><br>
<span style="font-weight:bold">Reply-To: </span>Ensembl developers list <<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>><br>
<span style="font-weight:bold">Date: </span>Wednesday, 7 May 2014 16:13<br>
<span style="font-weight:bold">To: </span>Ensembl developers list <<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [ensembl-dev] VEP using CADD plugin<br>
</div>
<div><br>
</div>
<div>
<div>
<div dir="ltr">Hello,
<div><br>
</div>
<div>Correct, the plugin was intended to work with the whole_genome_SNVs.tsv file, which only contains data for SNVs.</div>
<div><br>
</div>
<div>I've modified the plugin so that it should be able to cope with indel data files such as you have; please do let me know if you have any problems as I've only sparingly tested it on made-up data!</div>
<div><br>
</div>
<div>Regards</div>
<div><br>
</div>
<div>Will McLaren</div>
<div>Ensembl Variation</div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 7 May 2014 15:37, Genomeo Dev <span dir="ltr"><<a href="mailto:genomeodev@gmail.com" target="_blank">genomeodev@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi,
<div><br>
</div>
<div>There seem to be a discrepancy between the CADD score calculated using VEP with the CADD.pm plugin and the tabix direct output:</div>
<div><br>
</div>
<div>For example using this 1000G variant:</div>
<div><br>
</div>
<div>
<div>#CHROM<span style="white-space:pre-wrap"> </span>POS<span style="white-space:pre-wrap"></span>ID<span style="white-space:pre-wrap">
</span>REF<span style="white-space:pre-wrap"></span>ALT<span style="white-space:pre-wrap">
</span>QUAL<span style="white-space:pre-wrap"></span>FILTER<span style="white-space:pre-wrap">
</span>INFO</div>
<div>7<span style="white-space:pre-wrap"> </span>86214932<span style="white-space:pre-wrap"></span>rs140931361<span style="white-space:pre-wrap">
</span>TTACTC<span style="white-space:pre-wrap"></span>T<span style="white-space:pre-wrap">
</span>.<span style="white-space:pre-wrap"></span>PASS<span style="white-space:pre-wrap">
</span>.</div>
<div><br>
</div>
<div><a href="http://variant_effect_predictor.pl" target="_blank">variant_effect_predictor.pl</a> -i input.txt --format vcf --plugin CADD,/media/sf_D_DRIVE/Projects/Databases/CADD/v1.0/1000G.tsv.gz<br>
</div>
<div>does not return any CADD score</div>
<div><br>
</div>
<div>whereas </div>
<div>
<div>$ tabix -p vcf 1000G.tsv.gz 7:86214932-86214932</div>
<div>7<span style="white-space:pre-wrap"> </span>86214932<span style="white-space:pre-wrap"></span>TTACTC<span style="white-space:pre-wrap">
</span>T<span style="white-space:pre-wrap"></span>-0.420243<span style="white-space:pre-wrap">
</span>2.040</div>
</div>
<div><br>
</div>
<div>This seems to affect indels and not SNVs. I could see in the plugin that there is a rule to ignore indels. Any suggestions please how to safely change that?</div>
<div><br>
</div>
<div>Also, in the plugin, I assume there is a test to ensure the alleles are identical between the input file and the 1000G.tsv.gz file. Is this correct?</div>
<div><br>
</div>
<div>Thanks.</div><span class="HOEnZb"><font color="#888888">
<span><font color="#888888">
<div><br>
</div>
-- <br>
<div dir="ltr">G.</div>
</font></span></font></span></div><span class="HOEnZb"><font color="#888888">
</font></span></div><span class="HOEnZb"><font color="#888888">
<br>
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</font></span></blockquote>
</div>
<br>
</div>
</div>
</div>
</span>
</div>

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<br></blockquote></div><br></div>