CNVKIT_EXPORT(1)

✨ CNVKIT_EXPORT ✨

okay so bestie, welcome to cnvkit_export from section 1 of the User Commands manual, and no cap this one is a whole mood 💖

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🌸 NAME 🌸

cnvkit_export — convert CNVkit output files to another format. that's it, that's the job, and it ate 💅

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🦋 DESCRIPTION 🦋

the usage line, verbatim, because we do not play with syntax around here:

usage: cnvkit.py export [-h]

       {bed,seg,vcf,theta,nexus-basic,nexus-ogt,cdt,jtv,gistic}
              ...

so like. you pick one of those formats and it converts your stuff. simple as.

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🎀 positional arguments 🎀

these are the formats you can pick from, and the manpage says to use -h on them for more info (iykyk):

• {bed,seg,vcf,theta,nexus-basic,nexus-ogt,cdt,jtv,gistic} — the export formats. use with -h for more info, periodt.
• bed — convert segments to BED format. the input is a segmentation file (.cns) where, preferably, log2 ratios have already been adjusted to integer absolute values using the call command. so like, go run call first bestie, it's giving prepared ✨
• seg — convert segments to SEG format. compatible with IGV and GenePattern. iconic duo fr fr 🫶
• vcf — convert segments to VCF format. input is a segmentation file (.cns) where, preferably, log2 ratios have already been adjusted to integer absolute values using the call command. same energy as bed tbh 💀
• theta — convert segments to THetA2 input file format (*.input). very niche, very demure 🌸
• nexus-basic — convert bin-level log2 ratios to Nexus Copy Number "basic" format. lowercase name, uppercase vibe 👑
• nexus-ogt — convert log2 ratios and b-allele freqs to Nexus "Custom-OGT" format. two things at once, main character energy ⭐
• cdt — convert log2 ratios to CDT format. compatible with Java TreeView. nostalgic lowkey 🙈
• jtv — convert log2 ratios to Java TreeView's native format. the OG of the TreeView formats 💜
• gistic — yep, it's listed right there at the end, just sitting there by itself under jtv. the manpage is being mysterious about it, so we're being mysterious about it too 😭 not me leaving it exactly where I found it.

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💅 options 💅

• -h, --help — show this help message and exit. the classic. the legend. every single time 🎀

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ngl the only flag here is -h, so if you're looking for a secret extra option: there isn't one, bestie. the manpage said what it said 💀

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and that's the whole page!! shoutout to cnvkit.py export version 0.9.10, dated July 2023 — thank you for your service, you absolute icon 👑💖 bye bestie, go convert something slay ✨🦋