[ensembl-dev] Annotate tumor and normal read depth and variant allele frequency

[Will McLaren]

Hi Irsan,

In your run() subroutine, the following reference will contain the original
line of input:

$tva->base_variation_feature->{_line}

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).

Regards

Will McLaren
Ensembl Variation

On 4 January 2017 at 14:27, Irsan Kooi <irsankooi88 at gmail.com> wrote:

> Dear VEP developers,
>
> 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:
>
> READ_DEPTH_NORMAL = ...
> PERC_MUTATION_NORMAL = ...
> READ_DEPTH_TUMOR = ...
> PERC_MUTATION_TUMOR = ...
>
> So if you would consider this variant in my VCF file:
> #CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
>   FORMAT  NORMAL  TUMOR
> 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  0
> /0:9,0:0.00:0:0:.:309,0:5:4    0/1:0,7:1.00:2:5:0.714:0,229:0:0
>
> 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:
>
> package TumorNormalDepthAndVAF;
>
> use strict;
> use warnings;
>
> use base qw(Bio::EnsEMBL::Variation::Utils::BaseVepPlugin);
>
> sub version {
> return '0.1';
> }
>
> sub feature_types {
> return ['Transcript'];
> }
>
> sub get_header_info {
> my $self = shift;
> return {
> READ_DEPTH_NORMAL => 'Number of hiqh quality reads in NORMAL',
> PERC_MUTATION_NORMAL => 'Variant allele frequency in NORMAL',
> READ_DEPTH_TUMOR => 'Number of hiqh quality reads in TUMOR',
> PERC_MUTATION_TUMOR => 'Variant allele frequency in TUMOR',
> }
> }
>
> sub new {
> my $class = shift;
>
> my $self = $class->SUPER::new(@_);
>
> return $self;
> }
>
> sub run {
> my ($self, $tva) = @_;
> # add code to split 10th and 11th column by semi-colon, than extract 2nd
> and 3rd value of each and return
>
> return {
> READ_DEPTH_NORMAL => $someVar1,
> PERC_MUTATION_NORMAL => $someVar1,
> READ_DEPTH_TUMOR => $someVar1,
> PERC_MUTATION_TUMOR => $someVar1,
> };
> }
>
> 1;
>
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