samtools-quickcheck(1)

💅 NAME 💅

samtools quickcheck — a rapid sanity check on input files

ok so real talk, this is the samtools manual, section 1 (the "Bioinformatics tools" one, you already know 🧬), and we're talking about quickcheck — the little icon that just vibes in and tells you whether your files are even okay before you commit to anything heavy ✨

---

🌸 SYNOPSIS 🌸

samtools quickcheck [options] in.sam|in.bam|in.cram [ ... ]

---

🦋 DESCRIPTION 🦋

Quickly check that input files appear to be intact. That's the whole assignment, bestie 🫶

Here's what it actually does, step by step, no cap:

1. Checks that the beginning of the file contains a valid header (all formats) containing at least one target sequence
2. Then it seeks to the end of the file and checks that an end-of-file (EOF) is present and intact — BAM and CRAM only tho

the vibes are shallow on purpose — data in the middle of the file is not read, since that would be much more time consuming. So please note: this command will not detect internal corruption. It's literally just here to test that files aren't truncated before you do more intensive tasks on them. Think of it as a vibe check, not a full medical exam 💀

Exit codes, because they matter: this command will exit with a non-zero exit code if any input files don't have a valid header or are missing an EOF block. Otherwise it will exit successfully (with a zero exit code). Slay 💅

---

✨ OPTIONS ✨

• -v — Verbose output: will additionally print the names of all input files that don't pass the check to stdout. And the way that multiple -v options work? Each extra one causes additional messages regarding check results to be printed to stderr. So you can stack 'em for maximum yapping 📢
• -q — Quiet mode: disables warning messages on stderr about files that fail. Lowkey the "I don't wanna hear it" flag 🙈. If both -q and -v options are used then the appropriate level of -v takes precedence — so -v wins the argument, periodt.
• -u — Expect unmapped input data, so do not require targets in the header. Perfect for when your file is unmapped and you're not about to be judged for it 💖

---

👑 AUTHOR 👑

Written by Josh Randall from the Sanger Institute. Icon behavior, fr fr 🎀

---

🌈 SEE ALSO 🌈

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

---

ok that's the whole page, mwah 💋 this was samtools-1.24, dated 9 July 2026, and it's the samtools-quickcheck(1) girlies' moment — go check those files, bestie, ily 🫶💜