9.4 Parameters on Sites

Parameter	Description	Default
--window value	Window-size	1000000 bp
--window windows.bed	List of windows to use	see above
--readUpToDepth value	Depth up-to which bases are to be considered, ignore additional bases	1000
--filterDepth range	Filter out sites where sequencing depth is outside the range	Keep all
--filterCpG	Filter out CpG sites	keep CpG sites
--downsampleSites prob	Downsample sites with probability prob	don’t downsample