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samtools-phase(1) Bioinformatics tools samtools-phase(1) 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 website: <http://www.htslib.org/> samtools-1.23.1 18 March 2026 samtools-phase(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | AUTHOR | SEE ALSO
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