How to convert common genomics file formats

Allie Hajian
  • Updated

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. 

  1. Interleaved FASTQ to paired FASTQ   
  2. Paired FASTQ to unmapped BAM (uBAM) 
  3. BAM to unmapped BAM  
  4. CRAM to BAM 

The Validate BAM workflow confirms proper formatting of SAM or BAM files.

How to find the workspace

1. Select Showcase from the dropdown menu at top left.Terra_Library_dropdown_Screen_Shot.png

2. Click on the Format Conversion filter (left column) and select Sequence-Format-Conversion from the list.

Find-Format-Conversion-featured-workspace-in-Showcase-Library_Screen_shot.png

 

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