--window integer_value |
To specify parsing window size. Windows must be at least as large as the max read length. Default = 100000 bp. |
--readUpToDepth integer_value |
To set read depth up-to which reads are to be considered and ignore additional bases. Default = 1000. |
--filterDepth integer_value1,integer_value2 |
To filter out sites with sequencing depth outside the range [integer_value1,integer_value2]. Default = Will keep sites regardless of depth. |
--filterCpG |
To filter out CpG sites. Default = Will keep CpG sites. |
--maxRefN numeric_value |
To specify the max fraction of sites with reference=‘N’ in a window for the window to still be considered. numeric_value must be between 0 and 1 (inclusive). Default = 1. |
--maxMissing numeric_value |
To filter out windows which have more than the indicated data fraction missing. numeric_value must be between 0 and 1 (inclusive). Default = Will keep windows regardless of missingness. |