OncodriveFML: identifying coding and non-coding regions with cancer driver mutations

OncodriveFML is a method designed to analyze the pattern of somatic mutations across tumors in both coding and non-coding genomic regions to identify signals of positive selection, and therefore, their involvement in tumorigenesis. It can be used to identify protein-coding genes, promoters, untranslated regions, intronic splice regions, and lncRNAs-containing driver mutations.


Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
[user@cn3335 ~]$ module load oncodriveFML
[+] Loading singularity  3.10.5  on cn4338
[+] Loading oncodriveFML  2.2.0
[user@cn3335 ~]$ oncodrivefml -h
Usage: oncodrivefml [OPTIONS]

  Run OncodriveFML on the genomic regions in ELEMENTS FILE using the mutations

  -i, --input MUTATIONS_FILE      Variants file  [required]
  -e, --elements ELEMENTS_FILE    Genomic elements to analyse  [required]
  -t, --type [coding|noncoding]   Deprecated option
  -s, --sequencing [wgs|wes|targeted]
                                  Type of sequencing: whole genome, whole
                                  exome or targeted.
  -o, --output OUTPUT_FOLDER      Output folder. Default to regions file name
                                  without extensions.
  -c, --configuration CONFIG_FILE
                                  Configuration file. Default to
                                  'oncodrivefml_v2.conf' in the current folder
                                  if exists or to
                                  ~/.config/bbglab/oncodrivefml_v2.conf if
  --samples-blacklist SAMPLES_BLACKLIST
                                  Remove these samples when loading the input
  --signature SIGNATURE           File with the signatures to use
  --signature-correction [wg|wx]  Correct the computed signutares by genomic
                                  or exomic signtures. Only valid for human
  --no-indels                     Discard indels in your analysis
  --cores INTEGER                 Cores to use. Default: all
  --seed INTEGER RANGE            Set up an initial random seed to have
                                  reproducible results  [0<x<=4294967295]
  --generate-pickle               Deprecated flag. Do not use.
  --force                         Overwrite results if exists
  --debug                         Show more progress details
  --version                       Show the version and exit.
  -h, --help                      Show this message and exit.
Copy sample data to the current folder:
[user@cn3335 ~]$ cp $ODFML_DATA/* .
Run oncodriveFML on the sample data:
[user@cn3335 ~]$ oncodrivefml -i paad.txt.gz -e cds.tsv.gz --sequencing wes