Manual page from samtools-1.15
released on 21 February 2022


samtools phase – call and phase heterozygous SNPs


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


Call and phase heterozygous SNPs.



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]


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]


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


Written by Heng Li from the Sanger Institute.


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