NAME
samtools-phase - call and phase heterozygous SNPs
SYNOPSIS
samtools phase [-AF] [-k len] [-b prefix] [-q minLOD] [-Q minBaseQ] in.bam
DESCRIPTION
Call and phase heterozygous SNPs.
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, --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. |
AUTHOR
Written by Heng Li from the Sanger Institute.
SEE ALSO
Samtools website: <http://www.htslib.org/>;