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Adding parameters to support use of plugins #1

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merged 2 commits into from
Jul 5, 2024
Merged

Adding parameters to support use of plugins #1

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4f20d6b
add plugin support -test
allaway Jul 5, 2024
6d564c9
add some docs
allaway Jul 5, 2024
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50 changes: 48 additions & 2 deletions vcf2maf.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@

# Set any default paths and constants
my ( $tumor_id, $normal_id ) = ( "TUMOR", "NORMAL" );
my ( $vep_path, $vep_data, $vep_forks, $buffer_size, $any_allele, $inhibit_vep, $online, $vep_custom, $vep_config, $vep_overwrite, $vep_stats ) = ( "$ENV{HOME}/miniconda3/bin", "$ENV{HOME}/.vep", 4, 5000, 0, 0, 0, "", "", 0 , 0);
my ( $vep_path, $vep_data, $vep_forks, $buffer_size, $any_allele, $inhibit_vep, $online, $vep_custom, $vep_config, $vep_plugins, $vep_overwrite, $vep_stats ) = ( "$ENV{HOME}/miniconda3/bin", "$ENV{HOME}/.vep", 4, 5000, 0, 0, 0, "", "", "", 0 , 0);
my ( $ref_fasta ) = ( "$ENV{HOME}/.vep/homo_sapiens/112_GRCh37/Homo_sapiens.GRCh37.dna.toplevel.fa.gz" );
my ( $species, $ncbi_build, $cache_version, $maf_center, $retain_info, $retain_fmt, $retain_ann, $min_hom_vaf, $max_subpop_af ) = ( "homo_sapiens", "GRCh37", "", ".", "", "", "", 0.7, 0.0004 );
my $perl_bin = $Config{perlpath};
Expand Down Expand Up @@ -217,6 +217,7 @@ sub GetBiotypePriority {
'vep-forks=s' => \$vep_forks,
'vep-custom=s' => \$vep_custom,
'vep-config=s' => \$vep_config,
'vep-plugins=s' => \$vep_plugins,
'vep-overwrite!' => \$vep_overwrite,
'vep-stats' => \$vep_stats,
'buffer-size=i' => \$buffer_size,
Expand Down Expand Up @@ -478,6 +479,8 @@ sub GetBiotypePriority {
$vep_cmd .= " --custom $vep_custom" if ($vep_custom);
# Add --config if requested at command line
$vep_cmd .= " --config $vep_config" if ($vep_config);
# Add --plugin if requested at command line
$vep_cmd .= " --plugin $vep_plugins" if ($vep_plugins);
# Require allele match for co-located variants unless user-rejected or we're using a newer VEP
$vep_cmd .= " --check_allele" unless( $any_allele or $vep_script =~ m/vep$/ );
# Add --cache-version only if the user specifically asked for a version
Expand Down Expand Up @@ -526,6 +529,7 @@ sub GetBiotypePriority {
if ($retain_ann) {
push @ann_cols, split(',',$retain_ann);
}

my @ann_cols_format; # To store the actual order of VEP data, that may differ between runs
push( @maf_header, @ann_cols );

Expand Down Expand Up @@ -1279,6 +1283,10 @@ =head2 CUSTOMIZED OUTPUT

VEP config file to pass into vep's --config option [] (see L<CUSTOMIZED VEP ANNOTATION> below)

=item B<--vep-plugins>=I<VEP_PLUGIN_STRING>

A string of plugin instructions to pass into vep's --plugin option [] (see L<VEP PLUGINS> below)

=back

=head3 CUSTOMIZED VEP ANNOTATION
Expand All @@ -1291,7 +1299,7 @@ =head3 CUSTOMIZED VEP ANNOTATION

The custom VEP output is saved in the B<INFO> section of the VCF line, as part of the B<CSQ=> section.

To retain the customized output in the MAF file, in addition to specifing the custom annoation
To retain the customized output in the MAF file, in addition to specifing the custom annotation
and fields with B<--vep-custom> , we need to specify the fields to retain with B<--retain-ann>.

VEP's B<--custom>=I<STRING> is a comma-separated string:
Expand All @@ -1316,6 +1324,40 @@ =head3 CUSTOMIZED VEP ANNOTATION

=back

=head3 VEP PLUGINS

=over 2

**NOTE**: This currently has only been tested with the AlphaMissense plugin.
Other plugins, particularly custom plugins, may not be compatible.

VEP's plugins are described at:

L<https://useast.ensembl.org/info/docs/tools/vep/script/vep_plugins.html>

To use a VEP plugin, we need to specify the plugin name and options with B<--vep-plugins>.

For example, to use the VEP AlphaMissense plugin:

L<https://github.com/Ensembl/VEP_plugins/blob/main/AlphaMissense.pm>

After retrieving and tabix indexing the AlphaMissense database as described in the plugin README,
we can include these parameters and values in the vcf2maf command. Please note, you'll need to
specify the names of the annotations from the plugin that you would like to retain
with B<--retain-ann> to ensure they are included in the output MAF.

=over 8

--vep-plugin AlphaMissense,file=/path/to/AlphaMissense_{build}.tsv.gz

--retain-ann am_pathogenicity,am_class

=back

The output maf should now have the annotations am_pathogenicity and am_class included as columns.

=back

=head2 SUBPROCESSES

=head3 VEP CUSTOMIZATION
Expand Down Expand Up @@ -1399,6 +1441,10 @@ =head2 RELEVANT LINKS:

L<https://useast.ensembl.org/info/docs/tools/vep/script/vep_custom.html>

=item VEP plugins:

L<https://useast.ensembl.org/info/docs/tools/vep/script/vep_plugins.html>

=back

=head1 AUTHORS
Expand Down