CNVKIT_METRICS(1)

📦
version 0.9.13 · 3 versions
, in debian trixie, ubuntu noble, ubuntu questing, ubuntu resolute, ubuntu stonking

💖 CNVKIT_METRICS(1) 💖

okay bestie, welcome to cnvkit_metrics — it lives in the User Commands corner of your manual, and it's genuinely one of the most underrated glow-ups in the whole toolkit. iykyk 💅

✨ NAME ✨

cnvkit_metrics — compute coverage deviations and other metrics for self-evaluation. 🩷

🌸 DESCRIPTION 🌸

no cap, this is the part where you actually use it. here's the vibe:

usage: cnvkit.py metrics [-h] [-s SEGMENTS [SEGMENTS ...]]

[--drop-low-coverage] [-o FILENAME]
       cnarrays [cnarrays ...]
heads up — the usage line is written out exactly like that, blank line and all, so don't come for me about the formatting. it's giving faithful reproduction. ✨

🎀 positional arguments 🎀

  • cnarrays — one or more bin-level coverage data files. literally just hand it your *.cnn or *.cnr files. one or many, she can handle it. 🫶

💅 options 💅

  • -h, --help — show this help message and exit. the classic. the icon. the "help me bestie" button. 🙈
  • -s SEGMENTS [SEGMENTS ...], --segments SEGMENTS [SEGMENTS ...] — one or more segmentation data files (*.cns, which is the output of the segment command). now here's the tea 🍓: if you give more than one file, the number must match your coverage data files — and in that case the input files get paired together in the given order, like a lil matching game. otherwise, the same segments get used for all coverage files. slay, efficient. 👑
  • --drop-low-coverage — drop very-low-coverage bins before the calculations happen. why? to reduce the negative "fat tail" of bin log2 values in poor-quality tumor samples. it's literally just damage control for messy data. 💀
  • -o FILENAME, --output FILENAME — the output table file name. name your baby. name your output. ✨
real talk: those two quoted phrases — "fat tail" and "poorquality" — come straight from the source, so yes, the flag description keeps them exactly as-is. no editing, no notes. periodt.

and that's the whole page, bestie — every flag, every file type, every caveat, nothing skipped, nothing invented. 🦋

this lil manual moment is from cnvkit.py metrics 0.9.10, dated July 2023 — so if you're reading this in the future, congrats, you're time traveling. 🧚💜 stay hydrated, drop those low-coverage bins, and go get those metrics. mwah. 💖

📦 where this page comes from