NeuSomatic release 0.2.1

This release contains the following changes:

• Significant (2-3x) speed improvement for scanning alignment files.
• Lifted the MD tag requirement for input bam files.
• More program options added for scan_alignment (e.g. filter duplicate reads,...)
• An option is added for normalizing MQ, BQ, and other alignment channels for input candidate matrices
• New pre-trained models based on SEQC-II dataset are provided
• Update to Pytorch 1.1.0, torchvision 0.3.0, and cudatoolkit 9.0
• GPU training speed improvement by 25%.
• Minor fixes

NeuSomatic release 0.2.0

This release contains the following changes:

• Updating the Python version from Python 2.7 to Python 3.7.
• Updating the PyTorch version from 0.3.1 to 1.0.1
• Significant speed improvement for all steps such as preprocessing, training, calling.
• Several Bug fixes.
• More logging.

NeuSomatic release 0.1.4

This release contains the following changes:

• Several Bug fixes.
• Forward compatibility enabled for models trained using PyTorch v1.0.0.

NeuSomatic release 0.1.3

This release contains the following changes:

• Several Bug fixes.
• Significant speed improvement for scanning alignment files.
• Added allele frequency (AF), coverage, and read support information to output VCF.

NeuSomatic release 0.1.2

This release contains the following changes:

• Several Bug fixes.
• Improved speed and memory management for training large-scale datasets by merging the candidate .tsv files into larger inputs and use them iteratively.
• Added docker version of NeuSomatic https://hub.docker.com/r/msahraeian/neusomatic/ .
• Improved scan_alignments usability.
• Added maximum coverage limit to avoid out-of-memory problems.

NeuSomatic release 0.1.1

This release contains the following changes:

• Several Bug fixes.
• Traceback errors in multiprocessing mode and more clear error/exceptions handling and logging.
• Fixed the build script to work on Mac OS.
• Added docker pipelines to run other somatic mutation callers and a wrapper to merge their output for ensemble mode.
• Added a test example and a test script.

NeuSomatic release 0.1.0

Initial release of NeuSomatic.