Table 1.

Software versions and parameters used to generate the results

Software	Version	Parameters
HISAT2	2.0.4	–max-intronlen 300000 –novel-splicesite-
		outfile {output.novel_splice}
HISAT2_2PASS	2.0.4	–max-intronlen 300000 –novel-splicesite-
		infile {input.novel_splice}
		–novel-splicesite-outfile {output.novel_splice}
STAR	v2.5.2b	–twopassMode Basic –alignMatesGapMax
		300000
		–alignIntronMax 300000
STAR_fusion	v2.5.2b	–twopassMode Basic –alignMatesGapMax
		300000
		–alignIntronMax 300000 –chimSegmentMin
		–chimJunctionOverhangMin 12
		–chimSegmentReadGapMax 3
		12 –alignSJstitchMismatchNmax 5 -1 5 5
CRAC	2.5.0	-k 22 –detailed-sam –no-ambiguity –deep-snv
CRAC_fusion	2.5.0	-k 22 –detailed-sam –no-ambiguity –deep-
		snv –min-chimera-score 0
GATK	1.3.1	-T HaplotypeCaller -dontUseSoftClippedBases
		-stand_call_conf 20.0
		-stand_emit_conf 20.0
FREEBAYES	1.0.2	default
SAMTOOLS mpileup	1.3.1	default