Table 3:

BSBolt CallMethylation Parameters.

Option	Description
-I	Input BAM, input file must be in BAM format with index file
-DB	Path to index directory
-O	Output prefix
-remove-ccgg	Remove methylation calls in ccgg sites,default=False
-verbose	Verbose Output, default=False
-text	Output plain text files, default=False
-remove-sx	deprecated
-ignore-overlap	Only consider higher quality base when paired end reads overlap, default=False
-max	Max read depth to call methylation
-min	Minimum read depth required to report methylation site
-t	Number of threads to use when calling methylation values
-BQ	Minimum base quality for a base to considered for methylation calling, default=0
-MQ	Minimum alignment quality for an alignment to be considered for methylation calling, default=20
-CG	Only output CpG sites in CGmap file
-ATCG	Output ATCGmap file
-IO	Ignore orphans during methylation call