What if you tool takes an input format that isn't the same as the format of your data file? When you need to convert various sequencing file formats to GATK analysis ready input formats, we've got you covered.
This curated workspace has tools and instructions for converting the following formats so you can use your data in GATK analysis tools.
- Interleaved FASTQ to paired FASTQ files
- Paired FASTQ to unmapped BAM files
- BAM to unmapped BAM files
- CRAM to BAM files
The Validate BAM tool is also added to confirm proper formatting of SAM or BAM files.
You'll find the Sequence Format Conversion workspace in the Featured Workspace section of Terra's Showcase library:
- Select "Showcase" from the dropdown menu at top left:
- Select Sequence-Format-Conversion from the "Featured workspaces" list: