---
name: "sambamba-slice"
section: "1"
platform: "linux"
package: "sambamba"
version: "1.0.1+dfsg-2+b1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/sambamba-slice"
---

# sambamba-slice(1)

copying a slice of BAM file

## NAME

**sambamba-slice** - copying a slice of BAM file

## SYNOPSIS

**sambamba slice** *OPTIONS* \<input.bam\> *region*

## DESCRIPTION

Outputs reads overlapping specified region into new BAM file. (Default destination is STDOUT.) Input file must be coordinate-sorted and indexed.

While the same can be done with *sambamba-view*, that would be much slower due to a lot of compression/decompression work. Instead of naive method, *sambamba-slice* leverages knowledge about structure of BAM file and recompresses only a few BGZF blocks at the beginning and the end of the region, while the BGZF blocks in the middle are copied as is. As such, this tool doesn´t offer any options related to number of threads or compression level - most of the time is spent on I/O operations.

## OPTIONS

- **-o**, **--output-filename**=*OUTPUTFILE*

  Name of output file