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.