VARSCAN(1)

💅 VARSCAN — like, the manual page, bestie

so you found varscan(1), the User Commands girlie herself ✨ she does variant detection in next-generation sequencing data and honestly? she eats. let's get into it 🫶

🌸 NAME 🌸

varscan — variant detection in next-generation sequencing data 💖 that's the whole vibe.

✨ SYNOPSIS ✨

varscan [COMMAND] [OPTIONS]

like, command first, options after. iconic structure. no notes. 💅

🦋 DESCRIPTION 🦋

okay so. Variant detection in massively parallel sequencing. that's the job. here's the tea:

• For one sample, she calls SNPs, indels, and consensus genotypes.
• For tumor-normal pairs</> , she goes further and classifies each variant as Germline, Somatic, or LOH — and she also detects somatic copy number changes.

one tool, two whole personalities. main character energy fr fr 👑

🎀 USAGE 🎀

💜 COMMANDS:

okay bestie here's the full menu, every single one, no skips:

• pileup2snp — Identify SNPs from a pileup file
• pileup2indel — Identify indels a pileup file
• pileup2cns — Call consensus and variants from a pileup file
• mpileup2snp — Identify SNPs from an mpileup file
• mpileup2indel — Identify indels an mpileup file
• mpileup2cns — Call consensus and variants from an mpileup file
• somatic — Call germline/somatic variants from tumor-normal pileups
• copynumber — Determine relative tumor copy number from tumor-normal pileups
• readcounts — Obtain read counts for a list of variants from a pileup file
• filter — Filter SNPs by coverage, frequency, p-value, etc.
• somaticFilter — Filter somatic variants for clusters/indels
• processSomatic — Isolate Germline/LOH/Somatic calls from output
• copyCaller — GC-adjust and process copy number changes from VarScan copynumber output
• compare — Compare two lists of positions/variants
• limit — Restrict pileup/snps/indels to ROI positions

not me listing all fifteen like a good student 😭 every single command is here, we do NOT skip commands in this household 💀

🌈 SEE ALSO 🌈

the sacred link, the one you click when you need more:

http://varscan.sourceforge.net/using-varscan.html 🦋

and that's the page!! mwah 💋

this lil doc is from varscan 2.3.6, dated April 2014 — yes she's a vintage queen and she still slays 👑✨ bye bestie, go call some variants 🧚💖