CNVKIT(1)

📦
version 0.9.9 · 2 versions
, in ubuntu jammy

👑 CNVKIT(1) — the girlies' guide to the copy number toolkit ✨

okay so. bestie. this is cnvkit, and it lives in the User Commands section of the manual. she's a command-line toolkit for copy number analysis. that's the whole vibe. let's get into it 💅

🌸 NAME 🌸

cnvkit — a command-line toolkit for copy number analysis.

💖 DESCRIPTION 💖

okay so the usage is literally this, no cap, here's the exact shape of her:

usage: cnvkit [-h]

       {batch,target,access,antitarget,autobin,coverage,reference,fix,segment,call,diagram,scatter,heatmap,breaks,genemetrics,gainloss,sex,gender,metrics,segmetrics,bintest,import-picard,import-seg,import-theta,import-rna,export,version}
       ...

CNVkit, a command-line toolkit for copy number analysis. she contains multitudes 🦋

✨ positional arguments ✨

like, here's the whole squad. every single one of them, in order, periodt:

  • {batch,target,access,antitarget,autobin,coverage,reference,fix,segment,call,diagram,scatter,heatmap,breaks,genemetrics,gainloss,sex,gender,metrics,segmetrics,bintest,import-picard,import-seg,import-theta,import-rna,export,version} — these are the Sub-commands. throw -h at any of them for more info, iykyk 🔍

and here's the whole cast list with their little blurbs, because nobody gets left out:

  • batch — Run the complete CNVkit pipeline on one or more BAM files. the whole glow-up, start to finish 🌈
  • target — Transform bait intervals into targets more suitable for CNVkit. glow-up for your intervals 💫
  • access — List the locations of accessible sequence regions in a FASTA file. where can we actually go 🗺️
  • antitarget — Derive off-target ("antitarget") bins from target regions. the off-screen characters, but make them bins 🎭
  • autobin — Quickly calculate reasonable bin sizes from BAM read counts. she does the math so you don't have to 🧮
  • coverage — Calculate coverage in the given regions from BAM read depths. how deep does it go 💧
  • reference — Compile a coverage reference from the given files (normal samples). building the baseline, the control group, the normal friend 🧚
  • fix — Combine target and antitarget coverages and correct for biases. Adjust raw coverage data according to the given reference, correct potential biases and recenter. she's the therapist of the pipeline, correcting all the biases 😌
  • segment — Infer copy number segments from the given coverage table. connecting the dots, literally 🔗
  • call — Call copy number variants from segmented log2 ratios. saying it out loud 📢
  • diagram — Draw copy number (log2 coverages, segments) on chromosomes as a diagram. If both the raw probes and segments are given, show them side-by-side on each chromosome (segments on the left side, probes on the right side). art 🎨 left side segments, right side probes, no notes.
  • scatter — Plot probe log2 coverages and segmentation calls together. the two besties, side by side 🫶
  • heatmap — Plot copy number for multiple samples as a heatmap. everyone on one vibe board 🔥
  • breaks — List the targeted genes in which a copy number breakpoint occurs. where it all went down 💀
  • genemetrics — Identify targeted genes with copy number gain or loss. who's up, who's down 📈📉
  • sex — Guess samples' sex from the relative coverage of chromosomes X and Y. 🧬
  • metrics — Compute coverage deviations and other metrics for self-evaluation. the self-check, the mirror moment 🪞
  • segmetrics — Compute segment-level metrics from bin-level log2 ratios. zooming out, still counting 🔭
  • bintest — Test for single-bin copy number alterations. one bin, one test, one diva 💅
  • import-picard — Convert Picard CalculateHsMetrics tabular output to CNVkit .cnn files. The input file is generated by the PER_TARGET_COVERAGE option in the CalculateHsMetrics script in Picard tools. If 'antitarget' is in the input filename, the generated output filename will have the suffix '.antitargetcoverage.cnn', otherwise '.targetcoverage.cnn'. filename detective work, she reads the name and picks the suffix 🔎
  • import-seg — Convert a SEG file to CNVkit .cns files. translation era 🌐
  • import-theta — Convert THetA output to a BED-like, CNVkit-like tabular format. Equivalently, use the THetA results file to convert CNVkit .cns segments to integer copy number calls. two-for-one, she ate 🍽️
  • import-rna — Convert a cohort of per-gene log2 ratios to CNVkit .cnr format. rna girlies, this one's for you 🎀
  • export — Convert CNVkit output files to another format. leaving the group chat, going mainstream 📤
  • version — Display this program's version. her birth chart 🪐
heads up bestie: gainloss and gender are both chilling in the sub-command roster above ☝️ but this page gives them no blurb of their own. so don't come for me, I'm not making anything up 💀

🌟 optional arguments 🌟

  • -h, --help — show this help message and exit. the emergency bestie, always there 🫂

See the online manual for details: https://cnvkit.readthedocs.io — like, actually go read it, it's giving documentation ✨

and that's the page, bestie!! this version is cnvkit 0.9.9, dated October 2021, and the whole thing is filed under CNVKIT(1). stay slaying, run your pipelines, love u bye 💖🦋🌸

📦 where this page comes from