samtools-phase - call and phase heterozygous SNPs

       Written by Heng Li from the Sanger Institute.

       Call and phase heterozygous SNPs.

       samtools-phase - call and phase heterozygous SNPs

-A      Drop reads with ambiguous phase.

       -bSTR  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.

       -kINT  Maximum length for local phasing. [13]

       -qINT  Minimum Phred-scaled LOD to call a heterozygote. [40]

       -Q,--min-BQINT
               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.

samtools(1)

       Samtools website: <http://www.htslib.org/>

samtools-1.21                                   12 September 2024                              samtools-phase(1)

       samtools phase [-AF] [-klen] [-bprefix] [-qminLOD] [-QminBaseQ] in.bam