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.

NanoSV 1.2.4                                      October 2021                                         NANOSV(1)