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README.md

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Usage

Collect and add missing samples to data_clinical_sample.txt from genomic profiles.

Command Line

  -h, --help            show this help message and exit
  -d STUDYDIR, --study-directory=STUDYDIR
                        path to study directory
  -a, --add-missing-records
                        flag for adding missing records to clinical files
  -r, --remove-normal-records
                        flag for removing normal records from data files
  -o OUTPUTDIR, --output-data-directory=OUTPUTDIR
                        output directory used after removing normal records
                        from data

Example

mkdir path/to/output_folder
cd path/to/study
python report-missing-clinical-records.py -d . -ar -o path/to/output_folder

Notes

After the running script, the basic clinical info for the added sample should still be filled in, such as ONCOTREE_CODE