--filterMappingLength [integer_1,integer_2] |
To restrict the length of the mapped reads to the range [integer_1,integer_2]. Default = [0,200] |
--keepDuplicates |
To keep duplicate reads. Default = Duplicate reads are filtered out. |
--filterSoftClips |
To filter out Soft clipped reads. Default = Soft clipped reads are kept. |
--keepImproperPairs |
To keep Improper pairs. Default = Improper pairs are filtered out. |
--keepUnmappedReads |
To keep Unmapped reads. Default = Unmapped reads are filtered out. |
--keepFailedQC |
To keep reads that Failed QC. Default = reads that Failed QC are filtered out. |
--keepSecondaryReads |
To keep Secondary reads. Default = Secondary reads are filtered out. |
--keepSupplementaryReads |
To keep Supplementary reads. Default = Supplementary reads are filtered out. |
--filterReadsLongerThanFragment |
To filter out reads longer than fragment size. Default = Reads longer than fragment size are kept. |
--keepOnlyFwd or --keepOnlyRev |
To keep only forward or only reverse reads respectively. Default = Both forward and reverse reads are kept. |
--keepOnlyFirst or --keepOnlySecond |
To keep only the first Mate or keep only the second Mate respectively. Default = Both first and second Mates are kept. |
--blacklist blacklist.txt |
To filter out specific reads provided as a list. Default = nothing specific is filtered out. |
--filterMQ [integer1,integer2] |
To restrict the mapping quality of the reads to the range[integer1,integer2]. Default = Reads with all mapping quality are kept. |
--filterReadLength [integer1,integer2] |
To restrict the Read length to the range[integer1,integer2]. Default = Reads of all lengths are kept. |
--filterFragmentLength [integer1,integer2] |
To restrict the Fragment length to the range[integer1,integer2]. Default = Fragments of all lengths are kept. |