THetA2 Version 0.7

Released October 5, 2015

Version 0.7 introduces several optional, but highly recommend features. In particular, THetA2 can now do a priori clustering of intervals when information about potential germline SNPs is provided. As a result, THetA2 0.7 is much faster than the previous versions. See MANUAL.txt for full details

• Optional interval clustering a priori to running THetA2. This is highly recommended as it greatly reduces the run-time of the algorithm. NOTE: To run this option a user must provide SNP read count files. See MANUAL.txt.
• The matlab code to use BAF's to select between multiple solutions has been moved into the main python program.
• The default value for maximum normal contamination to consider has changed from 0.5 to 1.0.

THetA Version 0.6

Released April 11th, 2015

Version 0.6 introduces a new, simplified work-flow as well as support for whole-exome sequencing data. You may need to update scripts as the user interface has slightly changed. See MANUAL.txt for full details

• Added support for whole-exome sequencing data. See MANUAL.txt for instructions for whole-exome preprocessing.
• Simplified work-flow:
  • THetA now takes in full segmentation files* and automatically filters and selects intervals for processing, and provides copy number estimates for all intervals
  • Automatically considers both the case of one normal and one tumor sub-population, and one normal and two tumor sub-populations and selects best solution
  • If you have matlab installed, THetA now automatically outputs a pdf visualization plot of the results.
• Improved runtime performance when considering multiple tumor populations for many samples.

* For whole-genome sequencing, we now recommend running BIC-seq with the default parameters (i.e. lambda=2).