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.

Regions file format¶

The regions file is a text file with, at least, 4 columns separated by a tab character (the column order must be preserved):

Column 1 [CHROMOSOME]: Chromosome. A number between 1 and 22 or the letter X or Y (upper case)
Column 2 [START]: Start position. A positive integer.
Column 3 [STOP]: End position. A positive integer.
Column 4 [STRAND]: Strand: + for positive, - for negative, . for unknown.
Column 5 [ELEMENT]: Element identifier.
Column 6 [SEGMENT]: Segment identifier. Optional column.
Column 7 [SYMBOL]: Symbol, a different identifier for the element that will also be printed in the output file. Optional column.

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.