NAME

samtools phase - call and phase heterozygous SNPs

SYNOPSIS

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.