From a9317c08ceb21e1c75c536ca1e371b0b50525a88 Mon Sep 17 00:00:00 2001 From: dglemos Date: Wed, 3 Jul 2019 14:31:27 +0100 Subject: [PATCH] Update README with spdi and vcf_string info --- README.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index e4bdab491..612f40de0 100644 --- a/README.md +++ b/README.md @@ -162,6 +162,8 @@ Output is a JSON array of objects, one per input variant, with the following key * **hgvsg**: HGVS genomic nomenclature * **hgvsc**: HGVS transcript nomenclature * **hgvsp**: HGVS protein nomenclature +* **spdi**: Genomic SPDI notation +* **vcf_string**: VCF format (optional) * **warnings**: Warnings generated e.g. for invalid HGVS Use `--pretty` to pre-format and indent JSON output. @@ -187,6 +189,9 @@ Example output: "ENSP00000355627.4:p.Met268Thr", "NP_000020.1:p.Met268Thr" ], + "spdi" : [ + "NC_000001.11:230710047:A:G" + ], "warnings" : [ "Possible invalid use of gene name 'AGT' as HGVS reference; AGT:p.Met268Thr may resolve to multiple genomic locations" ] @@ -204,6 +209,6 @@ Example output: * `--grch37`: use GRCh37 assembly instead of GRCh38. * `--genomes`: set database parameters for [Ensembl Genomes](http://ensemblgenomes.org/) species. * `--pretty`: write pre-formatted indented JSON. -* `--fields [field1,field2]`: limit output fields. Comma-separated list, one or more of: `id`, `hgvsg`, `hgvsc`, `hgvsp`. +* `--fields [field1,field2]`: limit output fields. Comma-separated list, one or more of: `id`, `hgvsg`, `hgvsc`, `hgvsp`, `spdi`, `vcf_string`. * `--host [db_host]`: change database host from default `ensembldb.ensembl.org` (UK); geographic mirrors are `useastdb.ensembl.org` (US East Coast) and `asiadb.ensembl.org` (Asia). `--user`, `--port` and `--pass` may also be set. * `--pick`, `--per_gene`, `--pick_allele`, `--pick_allele_gene`, `--pick_order`: set and customise transcript selection process, see [VEP documentation](http://www.ensembl.org/info/docs/tools/vep/script/vep_other.html#pick)