NANOSV(1)

✨ NANOSV(1) — NanoSV, the Nanopore SV caller 💖

okay so bestie, NanoSV is a structural variant caller for the Nanopore 🧬✨ it's giving "find the big chromosome drama" energy and it is literally iconic 💅

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🌸 NAME

NanoSV — structural variant caller for the Nanopore 🦋

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🎀 SYNOPSIS

usage: NanoSV [-h] [-t THREADS] [-s SAMBAMBA] [-c CONFIG] [-b BED] [-o
OUTPUT]

              [-f SNP_FILE] [-v] bam

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🧚 DESCRIPTION

okay so the real tea is that the description is literally just "Put here a description." 💀 the devs said "I'll add it later" and we're all just vibing 🙈 but the usage line above is the main vibe check ✨

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💜 positional arguments

• bam — the path to your file, like /path/to/file.bam 🍓

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🔥 optional arguments

• -h, --help — shows the help message and exits, no cap 🫶
• -t THREADS, --threads THREADS — how many threads you want to use 🧵 the default is 4 ✨
• -s SAMBAMBA, --sambamba SAMBAMBA — give the full path to the sambamba or samtools executable 👑 the default is sambamba (note the trailing space in the original, it's giving quirky) 💅
• -c CONFIG, --config CONFIG — give the full path to your own ini file 📝 the default is config.ini 🌈
• -b BED, --bed BED — give the full path to your own bed file, used for coverage depth calculations 📊 the default is human_hg19.bed (trailing space again, we love a little chaos 🙈)
• -o OUTPUT, --output OUTPUT — give the full path to the output vcf file 🦄 the default is <stdout> 🖥️ (so if you don't pick one, it just spills into your terminal, iykyk 💀)
• -f SNP_FILE, --snp_file SNP_FILE — give the full path to the SNP variant file for phasing 🧬 supporting file formats are BED and VCF 💖
• -v, --version — shows the program's version number and exits 🎀

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🦋 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, you can run:

info NanoSV

and it should give you access to the complete manual 🫶

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NanoSV 1.2.4 · October 2021 · NANOSV(1) 🌈 slay, bestie, stay hydrated and keep your reads long 💖✨