Public Repository

Last pushed: a year ago
Short Description
Uses BAM files as input to produce a VCF (vcf.gz) with raw indel and SNV variant calls.
Full Description
  • Tool Version GATK3: 3
  • Working with Dockerized GATK3: Follow bellow steps to run GATK3 image from Docker Hub.
  1. Pull GATK3 image from Docker Hub

          #  sudo docker pull bd2kbdds/gatk3
    
  2. Build the image

       #  sudo docker build -t bd2kbdds/gatk3
    
  3. Run the image

       #  sudo docker run -i -t bd2kbdds/gatk3
    
  4. How to run GATK3 ?

        Look at: https://github.com/oicr-gsi/gatk3/tree/master/workflow-gatk3
        More details: https://software.broadinstitute.org/gatk/
    
Docker Pull Command
Owner
bd2kbdds

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