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DKFZ-ODCF / AlignmentAndQCWorkflows

The DKFZ alignment workflow plugin originally developed at the eilslabs
https://github.com/DKFZ-ODCF/AlignmentAndQCWorkflows/wiki
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Add collected ambiguously classified undirected WGBS reads in QC-JSON #47

Open vinjana opened 5 years ago

vinjana commented 5 years ago

Currently, reads whose orientation can not unambiguously be classified by WGBS_read_pair_reconstruction.py are simply ignored and no statistics are reported.

  1. Collect stats and add to QC-JSON
  2. Optional saving of ambiguously classified reads (for debugging and rescue attempts)