Quickstart
This document is intended for the impatient users who want to quickly setup and prioritize variants with SvAnna.
Prerequisites
SvAnna is written in Java 11 and needs Java 11+ to be present in the runtime environment. Please verify that you are using Java 11+ by running:
$ java -version
If java
is present on your $PATH
, then the command above will print a message similar to this one:
openjdk version "11" 2018-09-25
OpenJDK Runtime Environment 18.9 (build 11+28)
OpenJDK 64-Bit Server VM 18.9 (build 11+28, mixed mode)
Setup
SvAnna is installed by running the following three steps.
1. Download SvAnna distribution ZIP
Download and extract SvAnna distribution ZIP archive from here.
Expand the Assets menu and download the svanna-cli-${project.version}-distribution.zip
. Choose the latest stable version,
or a release candidate (RC).
After unzipping the distribution archive, run the following command to display the help message:
$ java -jar svanna-cli-${project.version}.jar --help
Note
If things went OK, the command above will print the following help message:
Structural variant prioritization
Usage: svanna-cli.jar [-hV] [COMMAND]
-h, --help Show this help message and exit.
-V, --version Print version information and exit.
Commands:
prioritize Prioritize the variants.
See the full documentation at `https://svanna.readthedocs.io/en/master`
2. Download SvAnna database files
SvAnna database files are available for download in the Downloads section.
After the download, unzip the archive(s) content into a folder of your choice and note down the path:
$ unzip -d svanna-data *.svanna.zip
Prioritize structural variants in VCF file
Let’s annotate a toy VCF file containing eight SVs reported in the SvAnna manuscript. First, let’s download the VCF file from here:
$ wget https://raw.githubusercontent.com/TheJacksonLaboratory/SvAnna/master/svanna-cli/src/examples/example.vcf
The variants were sourced from published clinical case reports and presence of each variant results in a Mendelian disease.
For the purpose of this test run, let’s assume that the VCF file contains SVs identified in a short/long read sequencing run of a patient presenting with the following clinical symptoms:
HP:0011890 - Prolonged bleeding following procedure
HP:0000978 - Bruising susceptibility
HP:0012147 - Reduced quantity of Von Willebrand factor
Now, let’s prioritize the variants:
$ java -jar svanna-cli-${project.version}.jar prioritize -d svanna-data --output-format html,csv,vcf --vcf example.vcf --phenotype-term HP:0011890 --phenotype-term HP:0000978 --phenotype-term HP:0012147
The variant Othman-2010-20696945-VWF-index-FigS7
disrupts a promoter of the von Willenbrand factor
(VWF) gene (Othman et al., 2010).
The variant receives the highest \(PSV\) score of 47.26, and it is ranked first.
SvAnna stores prioritization results in HTML, CSV, and VCF output formats in the current working directory.