Paco_0.1

Added support for plotting only chromosome 13, 18 and 21.

Paco

Changelog:

• Fixed: #14 and #15 by siongkong, missing penultimate bin from gc-count. Rerun all data for both reference and test samples if you update from a previous version, mixing data influences results negatively.
• Added: Guesstimate for maternal aberration. Provides the relative change in read depth from the expected amount over a series of bins and estimates start and end position of the CNV in outermost bins.
• Added: Interactive viewer for analysis through JSON object file and a local webpage. No data is transmitted to any server, allowing diagnostic usage.
• Added: Option to force block a whole chromosome in all reference data when using test.py, useful to test whether a certain chromosome is causing problems on other regions in the sample.
• Added: Simple pipeline that solves installation of packages and folder/file creation/dependencies itself. See run.sh.

Woodstock

First release of WISECONDOR.

Changes since pre-release version (wisecondor_130517_DB):

• Fixed: Missing imports for python2.6
• Fixed: Wrong value in AAD computation
• Fixed: Faulty removal of 'chr' prefix in consam.py when no prefix is present
• Changed: Default backend for matplotlib, now using 'agg'
• Changed: Plotting moved to separate script (plot.py)
• Removed: Useless, no longer supported qc scripts
• Several improvements in argument usage explanations

Please note:
Although the paper describes certain steps using SOAP2, this release uses BWA as mapper and converts from BAM files accordingly. If you want to use SOAP2 instead, please check the argument options for consam.py and add the appropriate columns for the needed information.

Also, the fix for the AAD computation changes the AAD results slightly: although removing a mistake, the paper does not reflect the actual computation anymore. In the paper and previous versions, the tested bin value was used to determine the relative change in read depth while this should be based on the values in the reference set, thus removing influences of aberrations. Changes in the AAD results should range from 0.001% to 0.01%, making the effect negligible.