When you need to convert various sequencing file formats to GATK analysis-ready input formats, we've got you covered. You'll find the Sequence Format Conversion workspace in the Featured Workspace section of Terra's Showcase library.
What's in the workspace
This curated workspace has tools and instructions for converting the following formats so you can use your data in GATK analysis workflows on Terra.
File conversion WDLs in the workspace
- Interleaved FASTQ to paired FASTQ
- Paired FASTQ to unmapped BAM (uBAM)
- BAM to unmapped BAM
- CRAM to BAM
The Validate BAM workflow confirms proper formatting of SAM or BAM files.
How to find the workspace
1. From the main navigation menu (top left), expand the Library section and select Featured Workspaces.
2. Click on the Format Conversion filter (left column - you may need to scroll down quite a bit) and select Sequence-Format-Conversion from the list.