NAME

NanoSV - structural variant caller for the Nanopore

DESCRIPTION

usage: NanoSV [-h] [-t THREADS] [-s SAMBAMBA] [-c CONFIG] [-b BED] [-o OUTPUT]
[-f SNP_FILE] [-v] bam
Put here a description.

positional arguments:

bam
/path/to/file.bam

optional arguments:

-h, --help
show this help message and exit
-t THREADS, --threads THREADS
Number of threads [default: 4]
-s SAMBAMBA, --sambamba SAMBAMBA
Give the full path to the sambamba or samtools executable [default: sambamba ]
-c CONFIG, --config CONFIG
Give the full path to your own ini file [ default: config.ini ]
-b BED, --bed BED
Give the full path to your own bed file, used for coverage depth calculations [default: human_hg19.bed ]
-o OUTPUT, --output OUTPUT
Give the full path to the output vcf file [default: <stdout> ]
-f SNP_FILE, --snp_file SNP_FILE
Give full path to the SNP variant file for phasing. Supporting file formats: BED and VCF
-v, --version
show program's version number and exit

SEE ALSO

The full documentation for NanoSV is maintained as a Texinfo manual. If the info and NanoSV programs are properly installed at your site, the command
info NanoSV
should give you access to the complete manual.