Man page - samtools-phase(1)
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apt-get install samtools
Manual
samtools-phase
NAMESYNOPSIS
DESCRIPTION
OPTIONS
AUTHOR
SEE ALSO
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
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-A |
Drop reads with ambiguous phase. |
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-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] |
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-F |
Do not attempt to fix chimeric reads. |
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-k INT |
Maximum length for local phasing. [13] |
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-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/>