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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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Calculate target region size from TARGET_REGION_FILE #58

Open vinjana opened 5 years ago

vinjana commented 5 years ago

It is a nuissance having to add target region size, although it can simply and efficiently be calculated from the input target region file.

  1. Merge overlapping regions (BAM reads are counted only once even when overlapping multiple target region features, consequently the size is effectively the size of the covered regions)
  2. Calculate the total size of the regions covered by target regions.