This app was exported from precisionFDA (
It was created by George Asimenos, precisionFDA.

What’s this?

This is an example app that shows how to run HaplotypeCaller from GATK 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