NANOSV

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

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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.