NAME

       svim - Structural variant caller for long sequencing reads

DESCRIPTION

       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").

   positional arguments:
       {reads,alignment}
              modes

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

       alignment
              Detect SVs from an existing alignment

   optional arguments:
       -h, --help
              show this help message and exit

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

AUTHOR

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