4. Input files

FusionVet needs two types of input files.

4.1. BAM file

BAM file must be sorted and indexed using samtools

4.2. gene fusion file

The gene fusion file is a plain text file with 8 columns separated by space or tab (The first 4 columns describe the “chrom”, “transcription_start”, “transcription_end” and “symbol” of gene-1, the other 4 columns describe the same information for gene-2. Below example file defines two fusions:

chr21   39739182        40033704        ERG     chr21   42836477        42880085        TMPRSS2
chr14   38033152        38033701        EST14         chr7    13930855        14031050        ETV1