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.
samtools(1)
Samtools website: <
http://www.htslib.org/>