<div dir="ltr">Hi Irsan,<div><br></div><div>In your run() subroutine, the following reference will contain the original line of input:</div><div><br></div><div>$tva->base_variation_feature->{_line}<br></div><div><br></div><div>Note if you are using the new ensembl-vep beta code, this will be an arrayref of data split by the tab character (or delimiter as set).</div><div><br></div><div>Regards</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><div class="gmail_quote">On 4 January 2017 at 14:27, Irsan Kooi <span dir="ltr"><<a href="mailto:irsankooi88@gmail.com" target="_blank">irsankooi88@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 style="word-wrap:break-word">Dear VEP developers,<br><br>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><br></div><div><div>READ_DEPTH_NORMAL = ...</div><div>PERC_MUTATION_NORMAL = ...</div><div>READ_DEPTH_TUMOR = ...</div><div>PERC_MUTATION_TUMOR = ...</div></div><div><br>So if you would consider this variant in my VCF file:</div><div>#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL TUMOR<br>chr1 3463076 . C T . PASS ECNT=1;HCNT=1;MAX_ED=.;MIN_<wbr>ED=.;NLOD=2.66;TLOD=22.56 GT:AD:AF:ALT_F1R2:ALT_F2R1:<wbr>FOXOG:QSS:REF_F1R2:REF_F2R1 <font color="#ff2600">0<wbr>/0:9,0:0.00:0:0:.:309,0:5:4 </font> <font color="#ff2600">0/1:0,7:1.00:2:5:0.714:0,229:<wbr>0:0</font><br><br>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></div><div><br></div><div><div>package TumorNormalDepthAndVAF;</div><div><br></div><div>use strict;</div><div>use warnings;</div><div><br></div><div>use base qw(Bio::EnsEMBL::Variation::<wbr>Utils::BaseVepPlugin);</div><div><br></div><div>sub version {</div><div><span class="m_304582235216261488Apple-tab-span" style="white-space:pre-wrap"> </span>return '0.1';</div><div>}</div><div><br></div><div>sub feature_types {</div><div><span class="m_304582235216261488Apple-tab-span" style="white-space:pre-wrap"> </span>return ['Transcript'];</div><div>}</div><div><br></div><div>sub get_header_info {</div><div><span class="m_304582235216261488Apple-tab-span" style="white-space:pre-wrap"> </span>my $self = shift;</div><div><span class="m_304582235216261488Apple-tab-span" style="white-space:pre-wrap"> </span>return {</div><div><span class="m_304582235216261488Apple-tab-span" style="white-space:pre-wrap"> </span>READ_DEPTH_NORMAL => 'Number of hiqh quality reads in NORMAL',</div><div><span class="m_304582235216261488Apple-tab-span" style="white-space:pre-wrap"> </span>PERC_MUTATION_NORMAL => 'Variant allele frequency in NORMAL',</div><div><span class="m_304582235216261488Apple-tab-span" style="white-space:pre-wrap"> </span>READ_DEPTH_TUMOR => 'Number of hiqh quality reads in TUMOR',</div><div><span class="m_304582235216261488Apple-tab-span" style="white-space:pre-wrap"> </span>PERC_MUTATION_TUMOR => 'Variant allele frequency in TUMOR',</div><div><span class="m_304582235216261488Apple-tab-span" style="white-space:pre-wrap"> </span>}</div><div>}</div><div><br></div><div>sub new {</div><div><span class="m_304582235216261488Apple-tab-span" style="white-space:pre-wrap"> </span>my $class = shift;</div><div><br></div><div><span class="m_304582235216261488Apple-tab-span" style="white-space:pre-wrap"> </span>my $self = $class->SUPER::new(@_);</div><div><br></div><div><span class="m_304582235216261488Apple-tab-span" style="white-space:pre-wrap"> </span>return $self;</div><div>}</div><div><br></div><div>sub run {</div><div><span class="m_304582235216261488Apple-tab-span" style="white-space:pre-wrap"> </span>my ($self, $tva) = @_;</div><div><span class="m_304582235216261488Apple-tab-span" style="white-space:pre-wrap"> </span></div><div><span class="m_304582235216261488Apple-tab-span" style="white-space:pre-wrap"> </span># add code to split 10th and 11th column by semi-colon, than extract 2nd and 3rd value of each and return</div><div><br></div><div><span class="m_304582235216261488Apple-tab-span" style="white-space:pre-wrap"> </span>return {</div><div><span class="m_304582235216261488Apple-tab-span" style="white-space:pre-wrap"> </span>READ_DEPTH_NORMAL => $someVar1,</div><div><span class="m_304582235216261488Apple-tab-span" style="white-space:pre-wrap"> </span>PERC_MUTATION_NORMAL => $someVar1,</div><div><span class="m_304582235216261488Apple-tab-span" style="white-space:pre-wrap"> </span>READ_DEPTH_TUMOR => $someVar1,</div><div><span class="m_304582235216261488Apple-tab-span" style="white-space:pre-wrap"> </span>PERC_MUTATION_TUMOR => $someVar1,</div><div><span class="m_304582235216261488Apple-tab-span" style="white-space:pre-wrap"> </span>};</div><div>}</div><div><br></div><div>1;</div></div></div><br>______________________________<wbr>_________________<br>
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