Files

File formats

Note

All the files can be compressed using GZIP (extension “.gz”), BZIP2 (extension “.bz2”) or LZMA (extension “.xz”)

Input file format

The variants file is a text file with, at least, 5 columns separated by a tab character (the header is required, but the order of the columns can change):

  • Column CHROMOSOME: Chromosome. A number between 1 and 22 or the letter X or Y (upper case)
  • Column POSITION: Mutation position. A positive integer.
  • Column REF: Reference allele [1].
  • Column ALT: Alternate allele [1].
  • Column SAMPLE: Sample identifier. Any alphanumeric string.
  • Column CANCER_TYPE: Cancer type. Any alphanumeric string. Optional.
  • Column SIGNATURE: User defined signature categories. Any alphanumeric string. Optional.

Mutations are expected to be in the positive strand.

Regions file format

The regions file is a text file with, at least, 4 columns separated by a tab character (header is required):

  • Column CHROMOSOME]: Chromosome. A number between 1 and 22 or the letter X or Y (upper case)
  • Column START: Start position. A positive integer.
  • Column END: End position. A positive integer.
  • Column ELEMENT: Element identifier. Can appear multiple times if the element is divided in segments.

Important

Analysis is perform element-wise. One single element can have multiple segments (even if you do not provide an identifier for them).

It is also important that different segments of the same element do not overlap.

Optional columns are:

  • Column STRAND: Strand: + for positive, - for negative, . for unknown.
  • Column SEGMENT: Segment identifier. Optional column.
  • Column SYMBOL: Symbol, a different identifier for the element that will also be printed in the output file. Optional column.

Signature file format

The signature file is a JSON file, where pairs of key-values represent the changes and the probabilities of those changes.

Changes are represented as AAA>C (reference triplet, > and alternate).

See the bgsignature package for more information.

Output file format

OncodriveFML generates a tabulated file with the results with the extension “.tsv”.

Check the output section to find a detailed description regarding the output.

[1](1, 2) The alleles consist on a single letter or a set of letters using A, C, G or T (upper case). Single Nucleotide Variants are indentified because both, REF and ALT contain only one letter. In Multi-Nucleotide Variants REF and ALT columns contain a set of letters of the same length. Insertions use - in the REF and a set of letters as ALT while deletions contain the set of deleted characters in the REF and - in the ALT columns.