This app was exported from precisionFDA (https://precision.fda.gov).
It was created by George Asimenos, precisionFDA.
What’s this?
This is an example app that shows how to run HaplotypeCaller from GATK 4.0.1.1. It uses the Spark-parallelized version of HaplotypeCaller and the hs37d5 reference genome.
What can it be used for?
Run this app to call variants on a BAM file.
Anything else?
Your input BAM file must be sorted. It is also a good idea to mark duplicates and recalibrate
This is a companion discussion topic for the original entry at registry.hub.docker.com/pfda2dockstore/gatk4-haplotypecallerspark-hs37d5/gatk4-haplotypecallerspark-hs37d5