Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
I am new to NGS analysis. I want to use BWA tool for alignment. How do I get the reference data GRCh37? I am interested in getting the latest version from Ensembl which is release 74. I do remember reading ..Do NOT use masked sequences. Are there instructions on creating own reference fasta files for the alignment? Also i do remember reading that it is very critical to prepare and index reference correctly.
Thanks so much.