samtools-phase - call and phase heterozygous SNPs
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.