Man page - samtools-phase(1)
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Manual
| samtools-phase(1) | Bioinformatics tools | samtools-phase(1) |
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(1)
Samtools website: <http://www.htslib.org/>
| 12 September 2024 | samtools-1.21 |