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

[Irsan Kooi]

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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