BAM2WIG(1)

💖 BAM2WIG(1) 💖

okay bestie, welcome to the BAM2WIG(1) manual page — yes it's a real one, yes it's giving bioinformatics main character energy, and yes i'm about to make it make sense. 🧬✨

---

🌸 NAME 🌸

bam2wig — convert bam files to wiggle files!! 🎀 and not just for the aesthetic, ok, it can also be used to generate exonpart hints for AUGUSTUS. slay.

---

✨ SYNOPSIS ✨

bam2wig [-r region] [-t trackname] <in.bam>

that's it. that's the whole vibe. 💅

---

🔥 OPTIONS 🔥

okay so before we even get to the flags, there's a whole prerequisite situation and it is NOT optional, bestie:

The file needs to be sorted by Reference ID (i.e. target name). like, it has to be. no cap.

To do that, use samtools sort <in.bam> — that's the move. 🫶

And to double check your file is actually sorted, hit it with samtools stats <in.bam> | grep 'is sorted' — it will literally tell you. 🙈

seriously, sort it first. unsorted input is not going to be your moment.

🦋 Parameters:

• -r — lets you specify a target region, e.g. 'chr3L:10-250'. tiny catch though: this option can only be used if an index file exists, see: samtools index. no index, no region, no exceptions. 😭
• -t — a string provided as track name. you name the track, the track gets named. iconic. 👑

---

💜 AUTHORS 💜

AUGUSTUS was written by M. Stanke, O. Keller, S. König, L. Gerischer and L. Romoth. absolute legends, we stan. 🌈⭐

---

📚 ADDITIONAL DOCUMENTATION 📚

An exhaustive documentation can be found in the file /usr/share/doc/augustus/README.md.gz. go read it, it's the extended cut. 🍓

---

and that's the page, bestie — BAM2WIG(1), from the AUGUSTUS crew, straight out of your friendly neighbourhood manual. mwah. 💖💅🦋