gdc-samtools-fastq
A WDL pipeline to convert GDC BAM files to fastq format utilizing GDC recommended options. For execution on Terra.bio.
GDC Samtools FASTQ Workflow
This WDL workflow converts aligned BAM files back into paired-end FASTQ format, adhering to GDC Data Harmonization standards. It is designed to run locally using the Dockstore CLI or in the cloud on Terra/AnVIL.
Overview
The workflow performs the following steps:
- Splits BAM by Read Group: Detects @RG tags in the B
This is a companion discussion topic for the original entry at github.com/AmyOlex/gdc-samtools-fastq/gdc-samtools-fastq