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samtools-phase.1
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'\" t
.TH samtools-phase 1 "2 September 2022" "samtools-1.16.1" "Bioinformatics tools"
.SH NAME
samtools phase \- call and phase heterozygous SNPs
.\"
.\" Copyright (C) 2008-2011, 2013-2018 Genome Research Ltd.
.\" Portions copyright (C) 2010, 2011 Broad Institute.
.\"
.\" Author: Heng Li <lh3@sanger.ac.uk>
.\" Author: Joshua C. Randall <jcrandall@alum.mit.edu>
.\"
.\" Permission is hereby granted, free of charge, to any person obtaining a
.\" copy of this software and associated documentation files (the "Software"),
.\" to deal in the Software without restriction, including without limitation
.\" the rights to use, copy, modify, merge, publish, distribute, sublicense,
.\" and/or sell copies of the Software, and to permit persons to whom the
.\" Software is furnished to do so, subject to the following conditions:
.\"
.\" The above copyright notice and this permission notice shall be included in
.\" all copies or substantial portions of the Software.
.\"
.\" THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
.\" IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
.\" FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
.\" THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
.\" LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
.\" FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
.\" DEALINGS IN THE SOFTWARE.
.
.\" For code blocks and examples (cf groff's Ultrix-specific man macros)
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.SH SYNOPSIS
.PP
samtools phase
.RB [ -AF ]
.RB [ -k
.IR len ]
.RB [ -b
.IR prefix ]
.RB [ -q
.IR minLOD ]
.RB [ -Q
.IR minBaseQ "] " in.bam
.SH DESCRIPTION
.PP
Call and phase heterozygous SNPs.
.SH OPTIONS
.TP 8
.B -A
Drop reads with ambiguous phase.
.TP 8
.BI -b \ STR
Prefix of BAM output. When this option is in use, phase-0 reads will be saved in file
.BR STR .0.bam
and phase-1 reads in
.BR 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
.BR STR .chimeric.bam.
[null]
.TP
.B -F
Do not attempt to fix chimeric reads.
.TP
.BI -k \ INT
Maximum length for local phasing. [13]
.TP
.BI -q \ INT
Minimum Phred-scaled LOD to call a heterozygote. [40]
.TP
.BI "-Q,\ --min-BQ " INT
Minimum base quality to be used in het calling. [13]
.TP
.BI --no-PG
Do not add a @PG line to the header of the output file.
.SH AUTHOR
.PP
Written by Heng Li from the Sanger Institute.
.SH SEE ALSO
.IR samtools (1)
.PP
Samtools website: <http://www.htslib.org/>