We have released Goby 3.0. There are a few novelties in this release that warranted a new major version:
- Goby 3 estimates probabilities that a genomic site contains a somatic mutation using adaptive models trained with DeepLearning4Java. Models are provided for RNA-Seq, paired exome and trio experimental design (subject and parents, with subject with possible de-novo mutations). See the companion project variationanalysis which we developed to train these models. New models can be trained with the companion project and used directly with Goby. These models can be used with the somatic_variation format of the discovery-sequence-variants mode. A preprint about the method is being finalized.
- We have enabled support for BAM and CRAM in the discovery-sequence-variant mode of Goby. This means that you can directly use BAM files to call somatic variations in them. CRAM support has not been well tested, but is supported by the HTSDK library that we also use to support BAM, so it will hopefully also work.
- We have upgraded Goby from an older version of the Java Samtools library to the latest HTSJDK (version 2.2.4). This may cause trouble with alignments in BAM format sorted with samtools 0.x. We discovered that HTSJDK will not recognize that these BAM files are sorted unless you modify the header or sort the BAM again with a recent version of samtools (1.x+).
- We ported the source code to Maven and consolidated dependencies. As a result you will find the goby-io jar in Maven Central, which makes it easier to use the Goby framework in any Maven project.
- The source code of the project has been moved to a new repository on GitHub: https://github.com/CampagneLaboratory/goby3