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.
What input files does the GATK accept / require?
Analyses done with the GATK typically involve several (though not necessarily all) of the following inputs:
- Reference genome sequence in FASTA format
- Unmapped sequencing data in uBAM format (alternative to FASTQ)
- Mapped sequencing data in SAM, BAM or CRAM format
- List of intervals
- Variant calls in VCF format or GVCF format (can be gzipped)
- Supplementary resources (e.g. known variants) as documented by the relevant tools