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

# samtools-phase(1)

call and phase heterozygous SNPs

## NAME

samtools-phase - call and phase heterozygous SNPs

## SYNOPSIS

samtools phase \[**-AF**\] \[**-k** *len*\] \[**-b** *prefix*\] \[**-q** *minLOD*\] \[**-Q** *minBaseQ*\] *in.bam*

## DESCRIPTION

Call and phase heterozygous SNPs.

## OPTIONS

- **-A**

  Drop reads with ambiguous phase.

- **-b** *STR*

  Prefix of BAM output. When this option is in use, phase-0 reads will be saved in file **STR**.0.bam and phase-1 reads in **STR**.1.bam. Phase unknown reads will be randomly allocated to one of the two files. Chimeric reads with switch errors will be saved in **STR**.chimeric.bam. \[null\]

- **-F**

  Do not attempt to fix chimeric reads.

- **-k** *INT*

  Maximum length for local phasing. \[13\]

- **-q** *INT*

  Minimum Phred-scaled LOD to call a heterozygote. \[40\]

- **-Q, --min-BQ** *INT*

  Minimum base quality to be used in het calling. \[13\]

- **--no-PG**

  Do not add a @PG line to the header of the output file.

## AUTHOR

Written by Heng Li from the Sanger Institute.

## SEE ALSO

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

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