Scroll to navigation

SVIM(1) User Commands 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
Detect SVs from raw reads. Align reads to given reference genome first.
Detect SVs from an existing alignment

optional arguments:

show this help message and exit
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.

July 2021 svim 2.0.0