COVTOBED(1)

✨ COVTOBED 💅 (that's section 1 of the manual, bestie)

okay so you know covtobed? It's a lil command-line girlie that turns the coverage track from a BAM file into a BED file. That's the whole vibe. She's in the User Commands chapter of the manual, and she's genuinely iconic at what she does. 🦋

🎀 NAME 🎀

covtobed — converts the coverage track from a BAM file into a BED file. no cap, that's literally the job description. 💖

🌸 SYNOPSIS 🌸

covtobed [options] [BAM]...

so you feed her some options, you feed her one (or more, she's flexible) BAM files, and she gives you the coverage. slay. ✨

💜 DESCRIPTION 💜

She computes coverage from alignments. That's it, that's the whole paragraph. short queen energy. 👑

🔥 OPTIONS 🔥

okay bestie, this is the part where you actually read stuff. every single flag, right here, no skips:

• -h, --help — shows you this help message and then exits, like a polite little angel. 🫶
• --version — shows the program's version number and then exits. quick vibe check on which covtobed you're running. ⭐
• --physical-coverage — computes physical coverage instead. heads up though: this one needs paired alignments in the input, so if your BAM isn't paired she cannot help you, sorry babe. 😭
• -q MINQ, --min-mapq=MINQ — skips any alignments whose mapping quality is less than MINQ. default is 0. lowkey a filter, highkey essential. 💅
• -m MINCOV, --min-cov=MINCOV — only prints a BED feature if the coverage is bigger than (or equal to) MINCOV. default is 0. so by default she's printing everything, but you can be picky if you want. 🎀
• -x MAXCOV, --max-cov=MAXCOV — only prints a BED feature if the coverage is lower than MAXCOV. default is 100000. yes, a hundred thousand. she said "cap". 🌈
• -l MINLEN, --min-len=MINLEN — only prints a BED feature if its length is bigger (or equal to) than MINLELN. default is 1. (the manual fr fr spells that placeholder MINLELN — I'm just the messenger, bestie 💀)
• -d, --discard-invalid-alignments — skips duplicates, failed QC, and non primary alignment, minq>0 (or whatever you set yourself if it's higher). default is 0. this is your "please throw out the messy ones" button. 🧚
• --output-strands — outputs coverage and stats separately for each strand. main character energy for your plus and minus strands, they don't have to share. 💖
• --format=CHOICE — sets the output format. you pick the CHOICE. 🦋

🌸 little reminder: options live in the same order she wrote them, and --format=CHOICE is last, so don't come for me about ordering. 🙈

and that's the page, babe. this manual is from covtobed version 1.1.4, dated September 2020 — vintage, but she still eats. periodt. 💅✨🎀