How to download and setup gatk
Open terminal and run command
git clone https://github.com/broadinstitute/gatk.git
git clone is used to create a copy or clone of gatk repositories.
You pass git clone a repository URL. it supports a few different network protocols and corresponding URL formats.
Also you may download zip file with gatk https://github.com/broadinstitute/gatk/archive/master.zip
Or simply clone gatk with SSH
[email protected]:broadinstitute/gatk.git
If you have some problems with gatk
You may open issue on gatk support forum (system) here: https://github.com/broadinstitute/gatk/issuesSimilar to gatk repositories
Here you may see gatk alternatives and analogs
cs-video-courses fastp dash deepvariant awesome-single-cell nextflow bwa khmer Awesome-Bioinformatics galaxy seqtk bioconda-recipes MultiQC hail minimap2 scipipe nucleus bioawk cromwell vsearch sambamba jbrowse bionode csvtk biojava deepTools circosJS containers salmon react-plotly.js