1samtools-phase(1)            Bioinformatics tools            samtools-phase(1)
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NAME

6       samtools phase - call and phase heterozygous SNPs
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SYNOPSIS

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

14       Call and phase heterozygous SNPs.
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OPTIONS

18       -A      Drop reads with ambiguous phase.
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20       -b STR  Prefix of BAM output. When this option is in use, phase-0 reads
21               will be saved in file STR.0.bam and phase-1 reads in STR.1.bam.
22               Phase unknown reads will be randomly allocated to  one  of  the
23               two  files.  Chimeric reads with switch errors will be saved in
24               STR.chimeric.bam.  [null]
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26       -F      Do not attempt to fix chimeric reads.
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28       -k INT  Maximum length for local phasing. [13]
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30       -q INT  Minimum Phred-scaled LOD to call a heterozygote. [40]
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32       -Q INT  Minimum base quality to be used in het calling. [13]
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34       --no-PG Do not add a @PG line to the header of the output file.
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AUTHOR

38       Written by Heng Li from the Sanger Institute.
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SEE ALSO

42       samtools(1)
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44       Samtools website: <http://www.htslib.org/>
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48samtools-1.13                     7 July 2021                samtools-phase(1)