GATK Mutect2 in wolF

Info

• Docker used: broadinstitute/gatk:4.1.4.1
• Reference files - including PON, come from GATK-best-practice bundle
• Original WDL for GATK 4.1.4.1 Best Practice
• Genome build: hg19
• Disk image:
  • NAME: mutect2-wolf
  • PROJECT: broad-cga-qing-gdac

News

A minimal implementation tested work, will add

• Build a disk image for all reference files, potentially as another task
• Cross-validate on Terra with same input
• Cost estimate
• Incorporates more optional arguments (bells and whistles)

Acknowledgement

Thanks to Aaron for building robust canine backend, to Julian for creating wolF and quick & responsive support.