---
name: "pgen_compress"
section: "1"
platform: "linux"
package: "plink2"
version: "2.00~a6.9-250129+dfsg-1+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/pgen_compress"
---

# pgen\_compress(1)

whole genome SNP analysis

## NAME

pgen\_compress-sse2 - whole genome SNP analysis

## DESCRIPTION

Usage: pgen\_compress \[-i\] \<input .bed or .pgen\> \<output filename\> \[sample\_ct\]

-

  \* sample\_ct is required when loading a .bed file \* **-i** causes the index to be saved to a separate .pgen.pgi file (usually it's

-

  embedded at the front of the .pgen); this is compatible with fully sequential .pgen writing

pgen\_compress **-u** \<input .pgen\> \<output .bed\>

pgen\_compress \[-i\] \<input .bed or .pgen\> \<output filename\> \[sample\_ct\]

-

  \* sample\_ct is required when loading a .bed file \* **-i** causes the index to be saved to a separate .pgen.pgi file (usually it's

-

  embedded at the front of the .pgen); this is compatible with fully sequential .pgen writing

pgen\_compress **-u** \<input .pgen\> \<output .bed\>

## SEE ALSO

The full documentation for **pgen\_compress-sse2** is maintained as a Texinfo manual.  If the **info** and **pgen\_compress-sse2** programs are properly installed at your site, the command

-

  **info pgen\_compress-sse2**

should give you access to the complete manual.