ESHG poster

1.2.0

Added some better in-code documentation

Group panelcn.MOPS calls

Output was unweildy and many calls for each CNV using panelcn.MOPS. Changed to grouped calling

Added panelcn.MOPS

Added panelcn.MOPS to the callers so final list of callers:

• CODEX2
• CopywriteR
• DECoN
• EXCAVATOR2
• ExomeDepth
• GATK v4.1
• panelcn.MOPS
• SavvyCNV
• XHMM

Ready for release to NHS study sites

Project set up and working for

• CODEX2
• CopywriteR
• DECoN
• EXCAVATOR2
• ExomeDepth
• GATK v4.1
• SavvyCNV
• XHMM

Tried and not being tested

• CANVAS (Not enough certainty to make any CNV calls as too few regions in targeted capture)
• WISExome (required modification of source code to work)
• CNVkit (failed on local data, if the issue can be identified might put back in)

CNVkit error:

Segmenting with method 'cbs', significance threshold 0.0001, in 1 processes
Exception in thread Thread-2:
Traceback (most recent call last):
  File "/usr/lib/python2.7/threading.py", line 801, in __bootstrap_inner
    self.run()
  File "/usr/lib/python2.7/threading.py", line 754, in run
    self.__target(*self.__args, **self.__kwargs)
  File "/usr/local/lib/python2.7/dist-packages/concurrent/futures/process.py", line 208, in _queue_management_worker
    result_item = result_queue.get(block=True)
  File "/usr/lib/python2.7/multiprocessing/queues.py", line 117, in get
    res = self._recv()
TypeError: __init__() takes exactly 2 arguments (1 given)