LUMPYEXPRESS(1)

💖 LUMPYEXPRESS(1) — the lumpyexpress glow-up 💖

okay bestie, sit down, hydrate, and let me tell you about lumpyexpress, a User Commands legend. it's the automated breakpoint detection girlie for standard analyses, and she is so much easier than her big sister lumpy. no cap. 🦋

✨ NAME ✨

lumpyexpress — Automated breakpoint detection for standard analyses 💅

🌸 SYNOPSIS 🌸

lumpyexpress [options]

that's it. that's the whole vibe. options go in, breakpoints come out. ✨

🎀 OPTIONS 🎀

okay this is the part where you actually pay attention, because every single one of these matters and I'm not letting you skim. 💖

• -B FILE — full BAM or CRAM file(s), comma separated if you've got more than one. This one is REQUIRED, bestie. no -B, no party. 🚫
• -S FILE — split reads BAM file(s), comma separated. 🧚
• -D FILE — discordant reads BAM file(s), comma separated. (yes the original really does say "files(s)", we love her anyway 🫶)
• -R FILE — an indexed reference genome fasta file. recommended for CRAMs, so if you're rolling with CRAMs and skipping this, that's a choice. 🙈
• -d FILE — a bedpe file of depths. comma separated, and each one is prefixed by sample:. for example:

sample_x:/path/to/sample_x.bedpe,sample_y:/path/to/sample_y.bedpe

• -o FILE — output file. default is fullBam.bam.vcf ⭐
• -x FILE — BED file to exclude. bye bye regions you don't care about 💀
• -P — output probability curves for each variant. data girlies rise 👑
• -m INT — minimum sample weight for a call. default 4. 🔥
• -r FLOAT — trim threshold. default 0. 🌸
• -T DIR — temp directory. default ./output_prefix.XXXXXXXXXXXX (yes those X's are real, that's the placeholder vibe) 🎀
• -k — keep temporary files. for the girlies who can't let go 🫶
• -K FILE — path to the lumpyexpress.config file. (default: same directory as lumpyexpress) 🌈
• -v — verbose. she will tell you EVERYTHING 💅
• -h — show this message. the classic cry for help button 😭

and then, right there in the middle of the options, the manpage just hits you with:

Error: -B is required

fr fr. it's not a suggestion, it's a whole personality. -B or nothing. 💀

👑 AUTHOR 👑

This manpage was written by Andreas Tille for the Debian distribution, and it can be used for any other usage of the program. 🫶

okay that's the whole page, you're officially certified. go detect some breakpoints, bestie. mwah. 💖✨

signing off from lumpyexpress 0.3.0, dated June 2020 — she's vintage, she's iconic, she's LUMPYEXPRESS(1). 🎀🦋