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Update G2P plugin docs #977

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Update G2P plugin docs
dglemos Jul 14, 2026
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dglemos Jul 31, 2026
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45 changes: 27 additions & 18 deletions docs/htdocs/info/docs/tools/vep/script/vep_plugins.html
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Expand Up @@ -526,45 +526,54 @@ <h2 id="plugins_existing">Existing plugins</h2>
./vep -i variations.vcf --plugin FunMotifs,/path/to/funmotifs/all_tissues.bed.gz,uterus
./vep -i variations.vcf --plugin FunMotifs,/path/to/funmotifs/blood.funmotifs_sorted.bed.gz,fscore,dnase_seq</p><p>Parameters Required:</p><p>[0] : FunMotifs BED file
[1]+ : List of columns to include within the output (e.g. fscore, skin, contactingdomain)</p><p></pre></p></p></div></td><td><div class="vdoc_dtype_count" style="white-space:normal;float:left;padding:2px 6px;cursor:default;background-color:#DAA520">Motif</div></td><td>-</td><td>Ensembl</td></tr>
<tr id="G2P" class="bg2 plugin_row" data-category="phenotype_data_and_citations"><td><div style="font-weight:bold"><a rel="external" href="https://github.com/Ensembl/VEP_plugins/blob/release/[[SPECIESDEFS::ENSEMBL_VERSION]]/G2P.pm">G2P</a></div><div style="margin-top:6px"><small>gene2phenotype</small></div></td><td><p> An Ensembl VEP plugin that uses G2P allelic requirements to assess variants in genes
<tr id="G2P" class="bg2 plugin_row" data-category="phenotype_data_and_citations"><td><div style="font-weight:bold"><a rel="external" href="https://github.com/Ensembl/VEP_plugins/blob/release/[[SPECIESDEFS::ENSEMBL_VERSION]]/G2P.pm">G2P</a></div><div style="margin-top:6px"><small>gene2phenotype</small></div></td><td><p> An Ensembl VEP plugin that uses G2P (www.ebi.ac.uk/gene2phenotype) allelic requirements to assess variants in genes

@likhitha-surapaneni likhitha-surapaneni Jul 27, 2026

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Do we want to add a hyperlink here?

@dglemos dglemos Jul 31, 2026

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I added the link

for potential phenotype involvement. <a class="button" href="#g2p" style="padding:3px 8px 0px 8px !important;height:18px" onclick="show_hide('g2p');" id="a_g2p">more</a></p><div id="div_g2p" style="display:none;word-wrap:break-word;"><p> The plugin has multiple configuration options, though minimally requires only
the CSV file of G2P data.
This Plugin is available for GRCh38 and GRCh37.</p><p> For further information see:
Thormann A, Halachev M, McLaren W, et al. Flexible and scalable diagnostic filtering of genomic variants using G2P with Ensembl VEP.
Nature Communications. 2019 May;10(1):2373. <a rel="external" href="https://doi.org/10.1038/s41467-019-10016-3">doi:10.1038/s41467-019-10016-3</a>. PMID: 31147538; PMCID: PMC6542828.</p><p> To improve performance, we recommend running VEP with multiple forks using the --fork &ltn&gt option where &ltn&gt
is the number of parallel processes. For the G2P plugin we recommend using 4 forks (--fork 4).</p><p> G2P data file:
To run the plugin it is necessary to provide a data file either downloaded from G2P or PanelApp.
The G2P file can be downloaded from:
To run the plugin it is necessary to provide an uncompressed data file downloaded from G2P, PanelApp or GenCC.
G2P files can be downloaded from:
<ul><li>Website <a href="https://www.ebi.ac.uk/gene2phenotype/download">https://www.ebi.ac.uk/gene2phenotype/download</a></li><li>API <a href="https://www.ebi.ac.uk/gene2phenotype/api/panel/&ltname&gt/download&nbsp">https://www.ebi.ac.uk/gene2phenotype/api/panel/&ltname&gt/download&nbsp</a>; Accepted panel names are: Cancer, Cardiac, DD, Ear, Eye, Skeletal, Skin (or <kbd>All</kbd> to download all panels in the same file)</p><p></li></ul><p> Options are passed to the plugin as key=value pairs, (defaults in parentheses):<table class="ss"><thead><tr><th>Argument</th><th>Description</th></tr></thead><tbody>
<tr class="bg1"><td><pre>file</pre></td><td>Path to G2P data file. The file needs to be uncompressed.
<tr class="bg2"><td><pre>variant_include_list</pre></td><td>A list of variants to include even if variants do not pass allele frequency filtering. The include list needs to be a sorted, bgzipped and
<tr class="bg1"><td><pre>file</pre></td><td>Path to the input data file. Supported formats are csv (G2P, GenCC) and tsv (PanelApp). The file needs to be uncompressed.</p><p><tr class="bg2"><td><pre>variant_include_list</pre></td><td>A list of variants to include even if variants do not pass allele frequency filtering. The include list needs to be a sorted, bgzipped and
tabixed VCF file.</p><p><tr class="bg1"><td><pre>af_monoallelic</pre></td><td>maximum allele frequency for inclusion for monoallelic genes (0.0001)
<tr class="bg2"><td><pre>af_biallelic</pre></td><td>maximum allele frequency for inclusion for biallelic genes (0.005)
<tr class="bg1"><td><pre>confidence_levels</pre></td><td>Confidence levels include: definitive, strong, moderate, limited Former confidence terms are still supported: confirmed, probable, possible, both RD and IF.
Separate multiple values with <kbd>&</kbd>.
<a href="https://www.ebi.ac.uk/gene2phenotype/terminology">https://www.ebi.ac.uk/gene2phenotype/terminology</a>
Default levels are confirmed and probable.</p><p><tr class="bg2"><td><pre>all_confidence_levels</pre></td><td>Set to 1 to include all confidence levels Setting the value to 1 will overwrite any confidence levels provided with the
confidence_levels option.</p><p><tr class="bg1"><td><pre>af_from_vcf</pre></td><td>set value to 1 to include allele frequencies from VCF file. Specifiy the list of reference populations to include with <kbd>--af_from_vcf_keys</kbd></p><p><tr class="bg2"><td><pre>af_from_vcf_keys</pre></td><td>VCF collections used for annotating variant alleles with observed allele frequencies. Allele frequencies are retrieved from VCF files. If
Default levels are definitive, strong and moderate (and former terms: confirmed, probable).</p><p><tr class="bg2"><td><pre>all_confidence_levels</pre></td><td>Set to 1 to include all confidence levels. Setting the value to 1 will overwrite any confidence levels provided with the
confidence_levels option.
Not recommended for diagnostic reporting.</p><p><tr class="bg1"><td><pre>af_from_vcf</pre></td><td>set value to 1 to include allele frequencies from VCF file. Specifiy the list of reference populations to include with <kbd>--af_from_vcf_keys</kbd></p><p><tr class="bg2"><td><pre>af_from_vcf_keys</pre></td><td>VCF collections used for annotating variant alleles with observed allele frequencies. Allele frequencies are retrieved from VCF files. If
af_from_vcf is set to 1 but no VCF collections are specified with <kbd>--af_from_vcf_keys</kbd>
all available VCF collections are included.
Available VCF collections: <kbd>topmed</kbd>, <kbd>uk10k</kbd>, <kbd>gnomADe</kbd>, <kbd>gnomADe_r2.1.1</kbd>, <kbd>gnomADg</kbd>, <kbd>gnomADg_v3.1.2</kbd>, <kbd>gnomADev4.1</kbd>, <kbd>gnomADgv4.1</kbd>.
Available VCF collections: <kbd>topmed</kbd>, <kbd>uk10k</kbd>, <kbd>gnomADe</kbd>, <kbd>gnomADe_r2.1.1</kbd>, <kbd>gnomADg</kbd>, <kbd>gnomADg_v3.1.2</kbd>, <kbd>gnomADe_v4.1</kbd>, <kbd>gnomADg_v4.1</kbd>.
Separate multiple values with <kbd>&</kbd>.
VCF collections contain the following populations:
<ul><li><kbd>topmed</kbd> - TOPMed (available for GRCh37 and GRCh38).</li><li><kbd>uk10k</kbd> - ALSPAC, TWINSUK (available for GRCh37 and GRCh38).</li><li><kbd>gnomADe</kbd> & 'gnomADe_r2.1.1 & <kbd>gnomADev4.1</kbd> - gnomADe:AFR, gnomADe:ALL, gnomADe:AMR, gnomADe:ASJ, gnomADe:EAS, gnomADe:FIN, gnomADe:NFE, gnomADe:OTH, gnomADe:SAS (for GRCh37 and GRCh38 respectively).</li><li><kbd>gnomADg</kbd> & <kbd>gnomADg_v3.1.2</kbd> & <kbd>gnomADgv4.1</kbd> - gnomADg:AFR, gnomADg:ALL, gnomADg:AMR, gnomADg:ASJ, gnomADg:EAS, gnomADg:FIN, gnomADg:NFE, gnomADg:OTH (for GRCh37 and GRCh38 respectively).&nbsp; Need to use <kbd>af_from_vcf</kbd> parameter to use this option. </p><p><tr class="bg1"><td><pre></li></ul><p> only_vcf_freq</pre></td><td>set to 1 to only use frequency from vcf files, can only be set if af_from_vcf is set. N/B - frequency information may be lost if this option is used </p><p><tr class="bg2"><td><pre>default_af</pre></td><td>default frequency of the input variant if no frequency data is found (0). This determines whether such variants are included;
the value of 0 forces variants with no frequency data to be
included as this is considered equivalent to having a frequency
of 0. Set to 1 (or any value higher than <kbd>af</kbd>) to exclude them.</p><p><tr class="bg1"><td><pre>types</pre></td><td>SO consequence types to include. Separate multiple values with <kbd>&</kbd> (splice_donor_variant, splice_acceptor_variant, stop_gained,
<ul><li><kbd>topmed</kbd> - TOPMed (available for GRCh37 and GRCh38).</li><li><kbd>uk10k</kbd> - ALSPAC, TWINSUK (available for GRCh37 and GRCh38).</li><li><kbd>gnomADe</kbd> & <kbd>gnomADe_r2.1.1</kbd> & <kbd>gnomADe_v4.1</kbd> - gnomADe:AFR, gnomADe:ALL, gnomADe:AMR, gnomADe:ASJ, gnomADe:EAS, gnomADe:FIN, gnomADe:NFE, gnomADe:OTH, gnomADe:SAS (for GRCh37 and GRCh38 respectively).</li><li><kbd>gnomADg</kbd> & <kbd>gnomADg_v3.1.2</kbd> & <kbd>gnomADg_v4.1</kbd> - gnomADg:AFR, gnomADg:ALL, gnomADg:AMR, gnomADg:ASJ, gnomADg:EAS, gnomADg:FIN, gnomADg:NFE, gnomADg:OTH (for GRCh37 and GRCh38 respectively).&nbsp; Need to use <kbd>af_from_vcf</kbd> parameter to use this option. </p><p><tr class="bg1"><td><pre></li></ul><p> only_vcf_freq</pre></td><td>set to 1 to only use frequency from vcf files, can only be set if af_from_vcf is set. N/B - frequency information may be lost if this option is used </p><p><tr class="bg2"><td><pre>types</pre></td><td>VEP SO consequence terms to include. Separate multiple values with <kbd>&</kbd>. This option replaces the default list. By default, the plugin uses:

@likhitha-surapaneni likhitha-surapaneni Jul 27, 2026 •
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Just a minor comment, there is an extra space before only_vcf_freq

@likhitha-surapaneni likhitha-surapaneni Jul 27, 2026

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VEP -> Ensembl VEP

@dglemos dglemos Jul 31, 2026

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Updated

splice_donor_variant, splice_acceptor_variant, stop_gained,
splice_donor_region_variant, splice_donor_5th_base_variant,
splice_region_variant, splice_polypyrimidine_tract_variant,
frameshift_variant, stop_lost, initiator_codon_variant,
inframe_insertion, inframe_deletion,missense_variant,
coding_sequence_variant, start_lost,transcript_ablation,
transcript_amplification, protein_altering_variant)</p><p><tr class="bg2"><td><pre>log_dir</pre></td><td>write stats to log files in log_dir
transcript_amplification, protein_altering_variant</p><p><tr class="bg1"><td><pre>add_types</pre></td><td>VEP SO consequence terms to append to the default types list. Separate multiple values with <kbd>&</kbd>.

@likhitha-surapaneni likhitha-surapaneni Jul 27, 2026

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VEP -> Ensembl VEP

@dglemos dglemos Jul 31, 2026

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Updated

This option cannot be used together with <kbd>types</kbd>.</p><p><tr class="bg2"><td><pre>log_dir</pre></td><td>write stats to log files in log_dir
<tr class="bg1"><td><pre>txt_report</pre></td><td>write all G2P complete genes and attributes to txt file
<tr class="bg2"><td><pre>html_report</pre></td><td>write all G2P complete genes and attributes to html file
<tr class="bg1"><td><pre>filter_by_gene_symbol</pre></td><td>set to 1 if filter by gene symbol. Do not set if filtering by HGNC_id.
This option is set to 1 when using PanelApp files. </p><p><tr class="bg2"><td><pre>filter_consequence_match</pre></td><td>to only report variants where the VEP predicted consequence matches the G2P variant consequence (GenCC term). Accepted values are:
<ul><li>broad: includes 'almost always', <kbd>probable</kbd> and <kbd>possible</kbd> matches</li><li>strict: includes 'almost always' and <kbd>probable</kbd> matches&nbsp; More details in <a href="https://europepmc.org/article/MED/37982373">https://europepmc.org/article/MED/37982373</a>
&nbsp; See here for the list of supported variant consequences in G2P: <a href="https://www.ebi.ac.uk/gene2phenotype/about/terminology#variant-consequence-section">https://www.ebi.ac.uk/gene2phenotype/about/terminology#variant-consequence-section</a></p><p><tr class="bg1"><td><pre></li></ul><p> flag_consequence_match</pre></td><td>flag if the VEP predicted consequence matches the G2P variant consequence (GenCC term). Accepted values are:
<ul><li>broad: includes 'almost always', <kbd>probable</kbd> and <kbd>possible</kbd> matches</li><li>strict: includes 'almost always' and <kbd>probable</kbd> matches&nbsp; More details in <a href="https://europepmc.org/article/MED/37982373">https://europepmc.org/article/MED/37982373</a></p><p><tr class="bg2"><td><pre></li></ul><p> only_mane</pre></td><td>set to 1 to ignore transcripts that are not MANE N/B - Information may be lost if this option is used.</p><p><tr class="bg1"><td><pre>include_disease</pre></td><td>set to 1 to report the G2P disease name in the VEP output. The disease name is not included in the G2P report files.</p><p></td></tr></tbody></table><p>
<tr class="bg1"><td><pre>filter_by_gene_symbol</pre></td><td>set to 1 if filtering by gene symbol. Do not set if filtering by HGNC_id.
This option is set to 1 automatically when using PanelApp files.</p><p><tr class="bg2"><td><pre>gencc_submitter</pre></td><td>Required when using a GenCC input file. Filters the GenCC file to rows whose submitted_as_submitter_name
matches this value.
Matching is case-insensitive.
Empty submitter names are not supported.</p><p><tr class="bg1"><td><pre>filter_consequence_match</pre></td><td>to only report variants where the VEP predicted consequence matches the G2P variant consequence term (GenCC term).
Accepted values are:
<ul><li>broad: includes 'almost always', <kbd>probable</kbd> and <kbd>possible</kbd> matches</li><li>strict: includes 'almost always' and <kbd>probable</kbd> matches&nbsp; This option is only supported with G2P input files.

@likhitha-surapaneni likhitha-surapaneni Jul 27, 2026

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Is the formatting as expected foralmost always ?

@dglemos dglemos Jul 31, 2026

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Updated

&nbsp; More details in <a href="https://europepmc.org/article/MED/37982373">https://europepmc.org/article/MED/37982373</a>
&nbsp; See here for the list of supported variant consequences in G2P:
&nbsp; <a href="https://www.ebi.ac.uk/gene2phenotype/about/terminology#variant-consequence-section">https://www.ebi.ac.uk/gene2phenotype/about/terminology#variant-consequence-section</a></p><p><tr class="bg2"><td><pre></li></ul><p> flag_consequence_match</pre></td><td>flag if the VEP predicted consequence matches the G2P variant consequence term (GenCC term).
Accepted values are:
<ul><li>broad: includes 'almost always', <kbd>probable</kbd> and <kbd>possible</kbd> matches</li><li>strict: includes 'almost always' and <kbd>probable</kbd> matches&nbsp; This option is only supported with G2P input files.
&nbsp; More details in <a href="https://europepmc.org/article/MED/37982373">https://europepmc.org/article/MED/37982373</a></p><p><tr class="bg1"><td><pre></li></ul><p> only_mane</pre></td><td>set to 1 to ignore transcripts that are not MANE N/B - Information may be lost if this option is used.</p><p><tr class="bg2"><td><pre>include_disease</pre></td><td>set to 1 to report the disease name from the input file in the VEP output. The disease name is not included in the G2P report files.</p><p></td></tr></tbody></table><p>
For more information - <a href="https://www.ebi.ac.uk/gene2phenotype/variant-filtering">https://www.ebi.ac.uk/gene2phenotype/variant-filtering</a></p><p> Example:
<pre class="code sh_sh">--plugin G2P,file=G2P.csv,af_monoallelic=0.05,types=<kbd>stop_gained&frameshift_variant</kbd>
--plugin G2P,file=G2P.csv,af_monoallelic=0.05,af_from_vcf=1
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