samtools-targetcut(1)

💅 samtools-targetcut(1) — bestie, it's a manual page

okay so this is the samtools-targetcut page from the samtools manual (section 1, bioinformatics tools, iykyk) — and it's a weird little niche icon, but we love her 💖

---

✨ NAME ✨

samtools targetcut — cut fosmid regions (for fosmid pool only) 🎀

🌸 SYNOPSIS 🌸

samtools targetcut [-Q minBaseQ] [-i inPenalty] [-0 em0] [-1 em1] [-2
em2] [-f ref] in.bam

🦋 DESCRIPTION 🦋

okay so what does this thing do. literally: it finds target regions by looking at how continuous the read depth is — like, it's vibing along the genome checking whether the depth keeps flowing or drops off, and that's how it decides where a target starts and ends. then it computes haploid consensus sequences for those targets, and outputs a SAM where each sequence corresponds to one target. one target = one sequence, slay ✨

if you've got option -f in use, then BAQ gets applied. noted. 🫶

🚨 real talk: this command is only designed for cutting fosmid clones from fosmid pool sequencing — that's per [Ref. Kitzman et al. (2010)]. so if you're trying to use it for literally anything else, that's not it bestie, please don't 😭

👑 OPTIONS 👑

• -Q minBaseQ — ignores bases whose quality is less than minBaseQ. mid quality? blocked, we don't see her 🙈
• -i inPenalty — the penalty for the in state transition. yes it's a penalty, no we don't make the rules 💀
• -0 em0 — emission score 0. that's the whole description, she's mysterious like that 🎀
• -1 em1 — emission score 1. number two of three, main character energy ⭐
• -2 em2 — emission score 2. and that's the last emission score, periodt 🔥
• -f ref — the reference FASTA file. also the thing that turns on BAQ, so she's kind of a big deal 🌈

💜 AUTHOR 💜

Written by Heng Li from the Sanger Institute. we stan 👑

🌟 SEE ALSO 🌟

• samtools(1)
• Samtools website: <http://www.htslib.org/>

---

and that's the whole page, bestie — no cap. this was samtools-targetcut(1) from samtools-1.24, dated 9 July 2026. go cut some fosmids, drink water, ily 🫶💖🧚