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Confirm or discard insertions (version 0.5.25)

Select dataset with filtered putative insertions:

Select datasets with all unfiltered insertions:

Select datasets with all unfiltered insertions from one or more control samples:

Output discarded records? Discarded records will be marked as failed.:

Minimum length necessary to match clip patterns:

If too low will create false matches, if too high will not find legitimate matches.

Usage: confirm_insertions [OPTIONS]

  Confirm insertions by checking that control file does not contain the same
  clipping pattern.

Options:
  -p, --putative_insertions_path PATH
                                  Path to file containing putative somatic
                                  insertions  [required]
  -t, --all_treatments_path PATH  Path to file containing all treatment
                                  insertions  [required]
  -c, --all_controls_path PATH    Path to file containing all control
                                  insertions  [required]
  -o, --output_path TEXT          Write annotated output to this Path.
  --output_discarded_records / --no_output_discarded_records
                                  Discard an alternative flag if the current
                                  read is in a proper pair.
  --version                       Show the version and exit.
  --help                          Show this message and exit.