PGEN_COMPRESS-SSE2(1)

💖 NAME 💖

pgen_compress-sse2 — whole genome SNP analysis, bestie. that's it, that's the vibe 🧬✨

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🎀 DESCRIPTION 🎀

okay so listen, here's literally how you run it:

pgen_compress [-i] <input .bed or .pgen> <output filename> [sample_ct]

and the tea you NEED to know:

• sample_ct is required when loading a .bed file — like, no sample_ct, no entry, sorry babe 😭
• -i makes the index get saved to a separate .pgen.pgi file (usually it's embedded at the front of the .pgen) — and it's compatible with fully sequential .pgen writing 🫶

and then there's the unconvert mode, the going-backwards one:

pgen_compress -u <input .pgen> <output .bed>

so yeah, -u takes a .pgen and gives you a .bed back. iconic honestly 💅

and fr fr, here's that first usage line again so you have it written down:

pgen_compress [-i] <input .bed or .pgen> <output filename> [sample_ct]

• sample_ct is required when loading a .bed file (yes, still 😌)
• -i → index gets saved to its own separate .pgen.pgi file, instead of being embedded at the front of the .pgen like it usually is — and yep, this plays nice with fully sequential .pgen writing 🌸

and one more time for the people in the back:

pgen_compress -u <input .pgen> <output .bed>

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✨ SEE ALSO ✨

the full documentation for pgen_compress-sse2 lives in a Texinfo manual 📖 — it's giving official, it's giving comprehensive, it's giving read-me-please. if the info and pgen_compress-sse2 programs are properly installed at your site, then this command:

info pgen_compress-sse2

should give you access to the complete manual 🌈. go get your knowledge, queen 👑

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and that's the whole page, bestie 🦋 — this was pgen_compress-sse2 Usage: from February 2026, filed under PGEN_COMPRESS-SSE2(1). take care of your genomes out there, mwah 💅💖