-.TH samtools 1 "15 November 2010" "samtools-0.1.10" "Bioinformatics tools"
+.TH samtools 1 "2 December 2010" "samtools-0.1.12" "Bioinformatics tools"
.SH NAME
.PP
samtools - Utilities for the Sequence Alignment/Map (SAM) format
.B OPTIONS:
.RS
.TP 8
+.B -A
+When used jointly with
+.B -r
+this option overwrites the original base quality.
+.TP 8
.B -e
Convert a the read base to = if it is identical to the aligned reference
base. Indel caller does not support the = bases at the moment.
command for details. [0]
.TP
.B -r
-Perform probabilistic realignment to compute BAQ, which will be used to
-cap base quality.
+Compute the BQ tag without changing the base quality.
.RE
.TP
.IP o 2
Dump BAQ applied alignment for other SNP callers:
- samtools calmd -br aln.bam > aln.baq.bam
+ samtools calmd -bAr aln.bam > aln.baq.bam
It adds and corrects the
.B NM