Argument	Synopsis (* = required)	Detail
Note: either --bam OR --fq1 & --fq2 arguments are required
--bam	*Input BAM file	Full path to a paired-end BAM file
--fq1	*Input fastq for read 1	Full path to a fastq / fastq.gz file for read 1
--fq2	*Input fastq for read 2	Full path to a fastq / fastq.gz file for read 2
--g	*Genome name	Name must match a folder in $SSDSGENOMESPATH
--n	Number of threads (for alignment step)	Default = 12
--r1BP	Trim size for read 1 (bp)	Integer value (default = 36)
--r2BP	Trim size for read 2 (bp)	Integer value (default = 40)
--splitSz	Large BAM files are split for ssDNA detection.	A lower value reduces the memory footprint (default = 20000000)
--outdir	Output folder	Defaults to BAM / FASTQ folder
--sample	Sample name for read group	-
--date	Date for read group	Date in DDMMYY format
--lane	Lane for read group	-
--bwaVers	Bwa version to use	0.5 or 0.7 [default]
--v	Use verbose mode	-
--h/help	Show help	-