samtools-phase1
Call and phase heterozygous snps
Usage
samtools phase
[-AF]
[-k
len]
[-b
prefix]
[-q
minLOD]
[-Q
minBaseQ]
in.bam
Overview
Call and phase heterozygous SNPs.
Options
-
-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.
|
Maximum length for local phasing. [13] |
|---|---|
|
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.
Releases
3 releases since Debian 11 (Bullseye); the text changed 2 times.
--min-BQ since Debian 12 (Bookworm);
-Q since Debian 12 (Bookworm).