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/>