SVIM(1)

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.