--filterMappingLength range |
To restrict the length of the mapped reads to the range. Default = [0,200] |
--filterReadLength range |
To restrict the Read length to the range. Default = keep all. |
--filterMQ range |
To restrict the mapping quality of the reads to the range. Default = keep all. |
--filterFragmentLength range |
To restrict the Fragment length to the range. Default = keep all. |
--filterPMDS range |
To restrict the PMDS score to the range. Default = keep all. |
--filterSoftClips range |
To filter out softclipped reads where the softclipped lengtht is outside the range. Default = keep all. |
--filterIndels range |
To filter out reads where the length of insertions and deletions is outside the range. Default = keep all. |
--filterMappingMismatches range |
To filter out reads where the mapping mismatches are outside of range. Default = keep all. |
--keepDuplicates |
To keep duplicate reads. Default = Duplicate reads are filtered out. |
--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. |
--filterWithAlternativeHits |
Filter out reads with alternative hits. Default = keep all. |
--blacklist blacklist.txt |
To filter out specific reads provided as a list. Default = nothing specific is filtered out. |
--keepReadsWithoutRG |
Keep reads without Readgroups. Default = filter out |
--readGroup list |
Only use reads belonging to list of Readgroups. Default = keep all |
--downsampleReads prob |
Downsample reads to given probability. |
--resetDuplicates |
Remove duplicate flags in read description. |
--markDuplicates |
Identify duplicates and mark one of the reads. |
--RGInfo rginfo.json |
File defining PMD and quality recalibration parameters. Default is no PMD and no quality recalibration. |
--pmd pmd_model |
Specify Post-mortem damage parameters. |
--recal recal_model |
Specify Quality score recalibration parameters. |