svim - Structural variant caller for long sequencing reads

        This manpage was written by Nilesh Patra for the Debian distribution and
        can be used for any other usage of the program.

svim 2.0.0                                          July 2021                                            SVIM(1)

       usage: svim [-h] [--version] {reads,alignment} ...

       SVIM  (pronounced  SWIM)  is  a structural variant caller for long reads.  It discriminates six different
       variant  classes:  deletions,  tandem  and  interspersed   duplications,   inversions,   insertions   and
       translocations. SVIM is unique in its capability of extracting both the genomic origin and destination of
       duplications.

       SVIM consists of four major steps: - COLLECT detects signatures for SVs in long read alignments - CLUSTER
       merges  signatures  that come from the same SV - COMBINE combines clusters from different genomic regions
       and classifies them into distinct SV types - GENOTYPE uses alignments spanning  SVs  to  determine  their
       genotype

       SVIM  can  process  two  types  of input. Firstly, it can detect SVs from raw reads by aligning them to a
       given reference genome first ("SVIM.py reads [options] working_dir reads genome").  Alternatively, it can
       detect SVs from existing reads alignments in SAM/BAM format  ("SVIM.py  alignment  [options]  working_dir
       bam_file").

   positionalarguments:
       {reads,alignment}
              modes

       reads  Detect SVs from raw reads. Align reads to given reference genome first.

       alignment
              Detect SVs from an existing alignment

   optionalarguments:-h, --help
              show this help message and exit

       --version, -v
              show program's version number and exit

       svim - Structural variant caller for long sequencing reads