Svync is a tool designed to synchronize structural variant calls from different callers. It uses YAML configs to define how to handle the standardization.
svync --config <config.yaml> --input <input.vcf>| Argument | Description |
|---|---|
--config/-c |
Path to the YAML config file |
--input/-i |
Path to the input VCF file |
| Argument | Description | Default |
|---|---|---|
--output/-o |
Path to the output VCF file | stdout |
--nodate/--nd |
Do not add the date to the output VCF file | false |
--mute-warnings/--mw |
Do not output warnings | false |
The configuration file is the core of the standardization in Svync. More information can be found in the configuration documentation.
This is the preffered way of installing BedGoVcf.
mamba install -c bioconda bedgovcfor with conda:
conda install -c bioconda bedgovcfPrecompiled binaries are available for Linux and macOS on the releases page.
Make sure you have go installed on your machine (or install it if you don't currently have it)
Then run these commands to install bedgovcf:
go get .
go build .
sudo mv bedgovcf /usr/local/bin/Next run this command to check if it was correctly installed:
bedgovcf --help