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)