svync

Svync is a tool designed to synchronize structural variant calls from different callers. It uses YAML configs to define how to handle the standardization.

Usage

svync --config <config.yaml> --input <input.vcf>

Arguments

Required

Argument	Description
--config/-c	Path to the YAML config file
--input/-i	Path to the input VCF file

Optional

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

Configuration

The configuration file is the core of the standardization in Svync. More information can be found in the configuration documentation.

Installation

Mamba/Conda

This is the preffered way of installing BedGoVcf.

mamba install -c bioconda bedgovcf

or with conda:

conda install -c bioconda bedgovcf

Precompiled binaries

Precompiled binaries are available for Linux and macOS on the releases page.

Installation from source

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