Update G2P plugin docs - #977
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| ./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 |
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Do we want to add a hyperlink here?
| 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). 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: |
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Just a minor comment, there is an extra space before only_vcf_freq
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VEP -> Ensembl VEP
| 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>. |
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VEP -> Ensembl VEP
| 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 This option is only supported with G2P input files. |
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Is the formatting as expected foralmost always ?
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Hi @dglemos , I have some minor comments.
Sandbox link: http://wp-np2-35.ebi.ac.uk:6080/info/docs/tools/vep/script/vep_plugins.html
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Update the plugin docs to reflect the latest G2P options update in the following PR Ensembl/VEP_plugins#844