iSeq Fusion Score

The score for fusion called with arriba is:

    score = 
        ln(split_reads1 + 1) + 
        ln(split_reads2 + 1) +
        2xln(discordant_mates + 1) +
        ln(1/8 x (coverage1 + coverage2 + 1)) +
        4 colocalization with a known fusion +
        3 for high confidence assigned by arriba +
        -5 for low confidence assigned by arriba +
        -3 for being out-of-frame +
        -3 for containing premature stop codon +
        -3 for head-to -head or tail-to-tail fusions

Fusions are filtered based on the above score (fusions with score equal to or higher than the threshold are kept):

• 7.5 threshold is used for highly sensitive fusion calling (default)

• 15 threshold is used for sensitive fusion calling

• 20 threshold is for specific fusion calling

For multiple fusions reported for the same fusion partners (and in the same orientation) only fusion with the highest score is kept.