samtools phase [-AF] [-k len] [-b prefix] [-q minLOD] [-Q minBaseQ] <in.bam>
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 INT
Minimum base quality to be used in het calling. [13]