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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.

References:

• Loris Mularoni, Radhakrishnan Sabarinathan, Jordi Deu-Pons, Abel Gonzalez-Perez and Núria López-Biga,
  OncodriveFML: a general framework to identify coding and non-coding regions with cancer driver mutations
  Genome Biology, 2016 17-128. DOI 10.1186/s13059-016-0994-0

• OncodriveFML Bitbucket repository
• OncodriveFML Documentation

• Module Name: oncodriveFML (see the modules page for more information)
• Unusual environment variables set
  • ODFML_HOME  installation directory
  • ODFML_BIN       executable directory
  • ODFML_DATA  sample data directory

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
  in MUTATIONS FILE.

Options:
  -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
                                  not.
  --samples-blacklist SAMPLES_BLACKLIST
                                  Remove these samples when loading the input
                                  file.
  --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
                                  genomes
  --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
...