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
options:
- -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.