MSC programs
produce_CI_CADD.py.txt (.py) - producing a confidence interval of disease-causing mutation raw CADD scores for each human gene. Output converted to Phred CADD scores. Note: remove .txt from file name to make usable.
ROC_CADD.r.txt (.r) - generating ROC curves, AUC and bootstrapping simulations to test the performance of CADD scores with fixed and MSC (per gene) cutoffs to differentiate false positives from true positives. Note: remove .txt from file name to make usable.
HGMD_CADD_full.txt - input file #1 for the produce_CI_CADD.py program.
conversion_table_range_v1.3.txt - input file #2 for the produce_CI_CADD.py program.
ROC_input_files.zip.txt - input files for the ROC_CADD.r program. Decompress and remove .txt from file name to make usable.
Files.zip.txt - all files of mixed proteins performance analysis. Including input files, scripts, summary files and figures. remove ".txt" and then extract the .zip file.
README.txt - description of all files in Files.zip.txt
VcfCheck.jar.txt - remove .txt before running. Converting ANNOVAR style '-' symbols of indels into a format readable by CADD. Usage on terminal: java -jar VcfCheck.jar normindel <Vcf_Input> <RefGenomeFasta> <Vcf_Output>
