samtools-phase(1)

✨ samtools-phase(1) ✨

okay so bestie, you're reading the samtools-phase(1) man page and honestly? it's a little cryptic in the original, so let me translate 💅

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🌸 NAME 🌸

samtools phase — calls and phases heterozygous SNPs. that's the whole vibe. call 'em, phase 'em, done. 🧬✨

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🦋 SYNOPSIS 🦋

samtools phase [-AF] [-k len] [-b prefix] [-q minLOD] [-Q minBaseQ]
in.bam

yes, it wraps, no, it's not a vibe check fail, that's just how manpages do 😭

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💖 DESCRIPTION 💖

Call and phase heterozygous SNPs. that's it, that's the description. short queen energy 👑

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🎀 OPTIONS 🎀

• -A — drops reads with ambiguous phase. like, if a read can't decide which team it's on, it gets benched. bye bestie 👋
• -b STR — the prefix for BAM output. when you turn this on, phase-0 reads get saved in the file STR.0.bam and phase-1 reads go in STR.1.bam. reads with unknown phase? they get randomly allocated to one of the two files (chaotic, i know, but that's the deal 🎲). chimeric reads with switch errors get saved in STR.chimeric.bam. default is [null].
• -F — do not attempt to fix chimeric reads. sometimes you just let them be messy, and that's valid 🫶
• -k INT — max length for local phasing. default is [13].
• -q INT — the minimum Phred-scaled LOD needed to call a heterozygote. default is [40].
• -Q, --min-BQ INT — minimum base quality to be used in het calling. default is [13].
• --no-PG — do not add a @PG line to the header of the output file. for when you want your header clean, no receipts 🧚‍♀️

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👑 AUTHOR 👑

Written by Heng Li from the Sanger Institute. legend behaviour, literally 🔥

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🌈 SEE ALSO 🌈

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

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k that's the whole page, go phase some SNPs, ily, don't forget to read samtools(1) too 🍓

samtools-1.24 · 9 July 2026 — that's the version and date stamp, mwah, see u in the group chat 💜✨