Impossible output, way more muts than it should

[Diogo Pellegrina]

I was running version 2.2.0 of oncodrivefml and this is one of the lines in my output file:

GENE_ID MUTS MUTS_RECURRENCE SAMPLES P_VALUE Q_VALUE P_VALUE_NEG Q_VALUE_NEG SNP MNP INDELS SYMBOL
IL32 167 2 2 1.5E-05 5.375E-05 0.999991 1 167 0 0 IL32

How can there be 167 mutations in 2 positions on 2 patients? The theoretical maximum should be 4. Looking at the imput file i've only managed to find 3 mutations on 2 positions on 2 patients.

The same problem appears in many other genes, often it also finds a gene mutated in many more samples than I'm expecting.

[Iker Reyes]

It seems that it is because the segments of your regions are overlapping and thus the same mutation gets analyzed multiple times. I will suggest to create non-overlapping regions.

We recently add this to the documentation (https://oncodrivefml.readthedocs.io/en/latest/files.html#regions-file-format).