CNVKIT_COVERAGE(1)

✨ CNVKIT_COVERAGE ✨

okay bestie, gather round, because this is cnvkit_coverage(1) from the User Commands girlies and she is literally here to calculate coverage in the given regions from BAM read depths. yes, that's the whole vibe. 🎀

---

💖 NAME 💖

cnvkit_coverage — calculate coverage in the given regions from BAM read depths. that's it, that's the girl. no cap. 💅

---

🌸 DESCRIPTION 🌸

so the usage is giving:

cnvkit.py coverage [-h] [-f FILENAME] [-c] [-q MIN_MAPQ] [-o FILENAME]
                   [-p [PROCESSES]]
                   bam_file interval

like, that's the whole shape of it. two positional besties and a lil pile of optional flags. slay. ✨

---

🦋 POSITIONAL ARGUMENTS 🦋

• bam_file — the mapped sequence reads, and yes she wants a .bam file. hand her your alignment, she'll do the rest. 🧚
• interval — the intervals you're obsessing over. either .bed or .list, pick your fighter. 💜

---

👑 OPTIONS 👑

• -h, --help — show this help message and exit. the classic. the icon. the "wait what does this do again" button. 🫶
• -f FILENAME, --fasta FILENAME — the reference genome, in FASTA format (think UCSC hg19.fa). lowkey essential for the FASTA-flavoured behaviour, so don't ghost her. 🌸
• -c, --count — get read depths by counting read midpoints within each bin. it's an alternative algorithm, so like, a whole different girl. 💅
• -q MIN_MAPQ, --min-mapq MIN_MAPQ — minimum mapping quality score (phred scale, 0-60) required to count a read toward coverage depth. [Default: 0] — so by default she's accepting everyone, no vibe check at the door. 😭
• -o FILENAME, --output FILENAME — output file name. name your baby. 🎀
• -p [PROCESSES], --processes [PROCESSES] — number of subprocesses to calculate coverage in parallel. give it no argument and she'll use the maximum number of available CPUs, main character energy fr fr. [Default: use 1 process] — so if you say nothing at all, it's just her, alone, doing one process. humble. 🌈

---

⭐ tiny reminder bestie: that -p flag takes an optional argument, which is why it's wrapped in brackets in the synopsis. don't come for me, come for the brackets. 💀

---

and that's the whole page, periodt. this was cnvkit.py coverage version 0.9.10, dated July 2023, filed under CNVKIT_COVERAGE(1) — mwah, go calculate some depths, i'm obsessed with you. 💖✨🦋