0.0.0

This is the first release of Guacamole!

The “somatic-standard” caller from this release competed in the ICGC-TCGA DREAM Mutation Calling Challenge (“guacamole.stock” on the Synthetic Challenge 4 Leaderboard).

This release focuses on:

• Infrastructure for working with aligned reads conveniently on Spark. Much of this is in DistributedUtil. This is implemented as a collection of higher-order functions that run a user supplied routine over the reads aligned to each genomic locus.
• The “somatic-standard” caller, a basic somatic variant caller that identifies somatic SNVs and indels by filtering the reads in various ways, applying a likelihood model to the tumor and normal pileups separately, calling variants where the likelihoods differ significantly, and optionally applying additional filters to the called variants.