-
--aligner <PROGRAM>
-
--ccs <PROGRAM>
-
--CCS-bam-file <PATH>
-
--ipd-model <MODEL>
-
--ipdsummary <PROGRAM>
-
--keep-temp-dir
-
--mappings <MAPPING>[ <MAPPING> ...]
-
--min-dna-seq-length <INT>
-
--min-relative-mapping-ratio <NUM>
-
--min-subreads-per-molecule <INT>
-
--modification-types <MOD-TYPE>
-
--nprocs-blasr <INT>
-
--num-simultaneous-ipdsummarys <INT>
-
--num-workers-per-ipdsummary <INT>
-
--only-produce-methylation-report
-
--partition <PARTITION:NUMBER-OF-PARTITIONS>
-
--pbindex <PROGRAM>
-
--quality-threshold <INT>
-
--verbose
|
-
-a <PROGRAM>
-
-C <PATH>
-
-c <PROGRAM>
-
-i <PROGRAM>
-
-l <INT>
-
-m <MAPPING>[ <MAPPING> ...]
-
-m <MOD-TYPE>
-
-M <MODEL>
-
-N <INT>
-
-n <INT>
-
-P <PARTITION:NUMBER-OF-PARTITIONS>
-
-p <PROGRAM>
-
-q <INT>
-
-r <INT>
-
-R <NUM>
-
-v
-
<ALIGNMENT-FILE>
-
<BAM-FILE>
|