---
name: "reapr-stats"
section: "1"
platform: "linux"
package: "reapr"
version: "1.0.18+dfsg-7"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/reapr-stats"
---

# reapr-stats(1)

generate REAPR stats from a BAM file

## NAME

reapr-stats - generate REAPR stats from a BAM file

## SYNOPSIS

**reapr stats** \[options\] \<preprocess-output-directory\> \<outprefix\>

## OPTIONS

- **-f** \<int\>

  Insert size \[ave from stats.txt\]

- **-i** \<int\>

  Minimum insert size \[pc1 from stats.txt\]

- **-j** \<int\>

  Maximum insert size \[pc99 from stats.txt\]

- **-m** \<int\>

  Maximum read length (this doesn’t need to be exact, it just determines memory allocation, so must be \>= max read length) \[2000\]

- **-p** \<string\>

  Name of .gz perfect mapping file made by **perfectmap**

- **-q** \<int\>

  Ignore reads with mapping quality less than this \[0\]

- **-s** \<int\>

  Calculate FCD error every n-th base \[ceil((fragment size) / 1000)\]

- **-u** \<string\>

  File containing list of chromosomes to look at (one per line)

## SEE ALSO

[reapr(1)](/reapr/1.md)