samtools phase [-AF] [-k len] [-b prefix] [-q minLOD] [-Q minBaseQ] in.bam
Call and phase heterozygous SNPs.
Drop reads with ambiguous phase.
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]
Do not attempt to fix chimeric reads.
Maximum length for local phasing. 
Minimum Phred-scaled LOD to call a heterozygote. 
Minimum base quality to be used in het calling. 
Do not add a @PG line to the header of the output file.
Written by Heng Li from the Sanger Institute.
Samtools website: <http://www.htslib.org/>
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