<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dear VEP developers,<br class=""><br class="">I am using a tumor-normal exome sequencing pipeline using MuTect2. To my knowledge, the default functionality of the variant effect predictor does not provide an option to annotate variants with the read depth and variant allele frequency for each the tumor and normal sample in the vcf. So I was planning to make a plugin that adds this information to the EXTRA column in the output in 4 key-value pairs:<div class=""><br class=""></div><div class=""><div class="">READ_DEPTH_NORMAL = ...</div><div class="">PERC_MUTATION_NORMAL = ...</div><div class="">READ_DEPTH_TUMOR = ...</div><div class="">PERC_MUTATION_TUMOR = ...</div></div><div class=""><br class="">So if you would consider this variant in my VCF file:</div><div class="">#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR<br class="">chr1 3463076 . C T . PASS ECNT=1;HCNT=1;MAX_ED=.;MIN_ED=.;NLOD=2.66;TLOD=22.56 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 <font color="#ff2600" class="">0/0:9,0:0.00:0:0:.:309,0:5:4 </font> <font color="#ff2600" class="">0/1:0,7:1.00:2:5:0.714:0,229:0:0</font><br class=""><br class="">The 10-th and 11-th column contain the information I want to appear in the extra column of the output. My problem is that I don’t know how I can access this information in my custom plugin, which looks something like:<br class=""></div><div class=""><br class=""></div><div class=""><div class="">package TumorNormalDepthAndVAF;</div><div class=""><br class=""></div><div class="">use strict;</div><div class="">use warnings;</div><div class=""><br class=""></div><div class="">use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);</div><div class=""><br class=""></div><div class="">sub version {</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>return '0.1';</div><div class="">}</div><div class=""><br class=""></div><div class="">sub feature_types {</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>return ['Transcript'];</div><div class="">}</div><div class=""><br class=""></div><div class="">sub get_header_info {</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>my $self = shift;</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>return {</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>READ_DEPTH_NORMAL => 'Number of hiqh quality reads in NORMAL',</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>PERC_MUTATION_NORMAL => 'Variant allele frequency in NORMAL',</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>READ_DEPTH_TUMOR => 'Number of hiqh quality reads in TUMOR',</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>PERC_MUTATION_TUMOR => 'Variant allele frequency in TUMOR',</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>}</div><div class="">}</div><div class=""><br class=""></div><div class="">sub new {</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>my $class = shift;</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>my $self = $class->SUPER::new(@_);</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>return $self;</div><div class="">}</div><div class=""><br class=""></div><div class="">sub run {</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>my ($self, $tva) = @_;</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span># add code to split 10th and 11th column by semi-colon, than extract 2nd and 3rd value of each and return</div><div class=""><br class=""></div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>return {</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>READ_DEPTH_NORMAL => $someVar1,</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>PERC_MUTATION_NORMAL => $someVar1,</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>READ_DEPTH_TUMOR => $someVar1,</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>PERC_MUTATION_TUMOR => $someVar1,</div><div class=""><span class="Apple-tab-span" style="white-space:pre"> </span>};</div><div class="">}</div><div class=""><br class=""></div><div class="">1;</div></div></body></html>