CNVKIT_AUTOBIN(1)

👑 CNVKIT_AUTOBIN 👑 — the cnvkit_autobin page, section 1 of the User Commands manual

okay bestie, buckle up, because this is the page for cnvkit_autobin and it's lowkey the vibe-checker of your CNV pipeline 🧚✨

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✨ NAME ✨

cnvkit_autobin — quickly calculate reasonable bin sizes from BAM read counts.

like. that's it. that's the whole job. it looks at your reads and goes "hmm, what bin size would actually make sense here" and then tells you. iconic behaviour honestly 💅

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🌸 DESCRIPTION 🌸

so the way you actually call this is:

usage: cnvkit.py autobin [-h] [-f FILENAME] [-m {hybrid,amplicon,wgs}]
                         [-g FILENAME] [-t TARGETS] [-b BP_PER_BIN]
                         [--target-max-size BASES] [--target-min-size BASES]
                         [--antitarget-max-size BASES] [--antitarget-min-size BASES]
                         [--annotate FILENAME] [--short-names]
                         [--target-output-bed FILENAME]
                         [--antitarget-output-bed FILENAME] bams [bams ...]

no cap, that's a lot of brackets. but don't panic, we're gonna go through every single one of them together 🫶

🎀 positional arguments 🎀

• bams — the sample BAM file(s) you wanna test for target coverage. yes, plural, you can throw more than one at it. it said bams [bams ...] and it meant it. 👑

🦋 options 🦋

• -h, --help — prints this help message and then dips. exit stage left. 🚪
• -f FILENAME, --fasta FILENAME — your reference genome, in FASTA format (think like UCSC hg19.fa). the blueprint, the source material, the moment. 🧬
• -m {hybrid,amplicon,wgs}, --method {hybrid,amplicon,wgs} — the sequencing protocol, and bestie, you have to pick one:
  • hybrid = hybridization capture
  • amplicon = targeted amplicon sequencing
  • wgs = whole genome sequencing

this is what decides whether and how to use antitarget bins. so it's not a cosmetic choice, it's a whole personality. [Default: hybrid]

• -g FILENAME, --access FILENAME — sequencing-accessible genomic regions, or the exons you wanna use as possible targets (like the output of refFlat2bed.py, for example). 💫
• -t TARGETS, --targets TARGETS — the potentially targeted genomic regions, e.g. all the possible exons for the reference genome. format: BED, interval list, etc. so many options, so much freedom. 🌈
• -b BP_PER_BIN, --bp-per-bin BP_PER_BIN — the desired average number of sequencing read bases mapped to each bin. [Default: 100000.0] — note the .0, it's giving float energy 🔥
• --target-max-size BASES — maximum size of target bins. [Default: 20000]
• --target-min-size BASES — minimum size of target bins. [Default: 20]
• --antitarget-max-size BASES — maximum size of antitarget bins. [Default: 500000]
• --antitarget-min-size BASES — minimum size of antitarget bins. [Default: 500]
• --annotate FILENAME — use gene models from this file to assign names to the target regions. format: UCSC refFlat.txt or ensFlat.txt file (preferred, the it-girl of formats), or BED, interval list, GFF, or similar. it's flexible like that 🎀
• --short-names — reduces multi-accession bait labels so they're short and consistent. the glow-up your labels deserve ✨
• --target-output-bed FILENAME — the filename for target BED output. if you don't specify one, it gets constructed from the input file basename. it'll figure itself out, she's resourceful 💅
• --antitarget-output-bed FILENAME — the filename for antitarget BED output. same deal: if you don't specify it, it's constructed from the input file basename. 🦋

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💖 pro tip from your girl: the defaults are there for a reason, so if you're not sure about the min/max sizes or BP_PER_BIN, just let them cook. no shame in trusting the default. 🫶

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and that's the whole page, bestie!! you absolutely ate this one 👑

this was cnvkit.py autobin version 0.9.10, from July 2023, and it lives in the User Commands section of the manual — mwah, stan, bye!! 💜🌸💅