To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

Default value of HaplotypeCaller

Hello Everyone,

I am working with gatk tool package "HaplotypeCaller" to find SNPs and Indels.
I want to know what are the initial default values of HaplotypeCaller, and can I change these values according to my need.

Thank you,


Sign In or Register to comment.