Collect and add missing samples to data_clinical_sample.txt
from genomic profiles.
-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
mkdir path/to/output_folder
cd path/to/study
python report-missing-clinical-records.py -d . -ar -o path/to/output_folder
After the running script, the basic clinical info for the added sample should still be filled in, such as ONCOTREE_CODE