avocado: A Variant Caller, Distributed

avocado is a distributed pipeline for calling variants, and is built on top of Apache Spark and the ADAM API. avocado provides a highly configurable pipeline that can be used for the alignment, processing, and variant calling of genomes/exomes/targets. We are currently in the process of hardening avocado for clincial use, and expanding the avocado pipeline so that it can triage processing steps based on genomic complexity.

avocado is on Github, and is in active development.


For support using avocado, please contact the avocado developer mailing list. Additionally, we track issues and feature enhancement requests through our Github issue tracker.


ADAM is available under the Apache 2 open source software (OSS) license. This OSS license is non-viral, and places no restrictions on users who would like to use or modify the software.