---
name: "lumpyexpress"
section: "1"
platform: "linux"
package: "lumpy-sv"
version: "0.3.1+dfsg-7+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/lumpyexpress"
---

# lumpyexpress(1)

Automated breakpoint detection for standard analyses

## NAME

lumpyexpress - Automated breakpoint detection for standard analyses

## SYNOPSIS

**lumpyexpress** \[options\]

## OPTIONS

- **-B** FILE

  full BAM or CRAM file(s) (comma separated) (required)

- **-S** FILE

  split reads BAM file(s) (comma separated)

- **-D** FILE

  discordant reads BAM files(s) (comma separated)

- **-R** FILE

  indexed reference genome fasta file (recommended for CRAMs)

- **-d** FILE

  bedpe file of depths (comma separated and prefixed by sample:) e.g sample\_x:/path/to/sample\_x.bedpe,sample\_y:/path/to/sample\_y.bedpe

- **-o** FILE

  output file \[fullBam.bam.vcf\]

- **-x** FILE

  BED file to exclude

- **-P**

  output probability curves for each variant

- **-m** INT

  minimum sample weight for a call \[4\]

**-r** FLOAT trim threshold \[0\]

- **-T** DIR

  temp directory \[./output\_prefix.XXXXXXXXXXXX\]

- **-k**

  keep temporary files

- **-K** FILE

  path to lumpyexpress.config file

-

  (default: same directory as lumpyexpress)

- **-v**

  verbose

- **-h**

  show this message

Error: **-B** is required

## AUTHOR

 This manpage was written by Andreas Tille for the Debian distribution and\
  can be used for any other usage of the program.