samtools-phase - Man Page

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

Call and phase heterozygous SNPs.

-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.

Written by Heng Li from the Sanger Institute.

samtools(1)

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

samtools(1).