---
name: "samtools-targetcut"
section: "1"
platform: "linux"
package: "samtools"
version: "1.21-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/samtools-targetcut"
---

# samtools-targetcut(1)

cut fosmid regions (for fosmid pool only)

## NAME

samtools-targetcut - cut fosmid regions (for fosmid pool only)

## SYNOPSIS

samtools targetcut \[**-Q** *minBaseQ*\] \[**-i** *inPenalty*\] \[**-0** *em0*\] \[**-1** *em1*\] \[**-2** *em2*\] \[**-f** *ref*\] *in.bam*

## DESCRIPTION

This command identifies target regions by examining the continuity of read depth, computes haploid consensus sequences of targets and outputs a SAM with each sequence corresponding to a target. When option **-f** is in use, BAQ will be applied. This command is **only** designed for cutting fosmid clones from fosmid pool sequencing \[Ref. Kitzman et al. (2010)\].

## OPTIONS

- **-Q** *minBaseQ*

  Ignore bases with quality less than *minBaseQ*.

- **-i** *inPenalty*

  Penalty for in state transition.

- **-0** *em0*

  Emission score 0.

- **-1** *em1*

  Emission score 1.

- **-2** *em2*

  Emission score 2.

- **-f** *ref*

  Reference FASTA file.

## AUTHOR

Written by Heng Li from the Sanger Institute.

## SEE ALSO

[*samtools*(1)](/samtools/1.md)

Samtools website: \<http://www.htslib.org/\>