Skip to content

Commit

Permalink
updated README
Browse files Browse the repository at this point in the history
  • Loading branch information
sigven committed Apr 27, 2023
1 parent 5ff3da5 commit c46e940
Showing 1 changed file with 4 additions and 4 deletions.
8 changes: 4 additions & 4 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -10,13 +10,13 @@
- [Getting started](#getting-started)
- [Contact](#contact)

### Overview {#overview}
### Overview

The generic variant annotator (*gvanno*) is a software package intended for simple analysis and interpretation of human DNA variants. Variants and genes are annotated with disease-related and functional associations. Technically, the workflow is built with the [Docker](https://www.docker.com) technology, and it can also be installed through the [Singularity](https://sylabs.io/docs/) framework.

*gvanno* accepts query files encoded in the VCF format, and can analyze both SNVs and short insertions or deletions (indels). The workflow relies heavily upon [Ensembl's Variant Effect Predictor (VEP)](http://www.ensembl.org/info/docs/tools/vep/index.html), and [vcfanno](https://github.com/brentp/vcfanno). It produces an annotated VCF file and a file of tab-separated values (.tsv), the latter listing all annotations pr. variant record. Note that if your input VCF contains data (genotypes) from multiple samples (i.e. a multisample VCF), the output TSV file will contain one line/record **per sample variant**.

### News {#news}
### News

- April 27th 2023 - **1.6.0 release**

Expand All @@ -39,7 +39,7 @@ The generic variant annotator (*gvanno*) is a software package intended for simp
- [Mutation hotspots](cancerhotspots.org) - Database of mutation hotspots in cancer
- [NHGRI-EBI GWAS Catalog](https://www.ebi.ac.uk/gwas/home) - Catalog of published genome-wide association studies (March 27th 2023)

### Getting started {#getting-started}
### Getting started

#### STEP 0: Prerequisites

Expand Down Expand Up @@ -186,6 +186,6 @@ Similar files are produced for all variants, not only variants with a *PASS* des

Documentation of the various variant and gene annotations should be interrogated from the header of the annotated VCF file. The column names of the tab-separated values (TSV) file will be identical to the INFO tags that are documented in the VCF file.

### Contact {#contact}
### Contact

sigven AT ifi.uio.no

0 comments on commit c46e940

Please sign in to comment.