-.TH samtools 1 "2 December 2010" "samtools-0.1.12" "Bioinformatics tools"
+.TH samtools 1 "16 March 2011" "samtools-0.1.14" "Bioinformatics tools"
.SH NAME
.PP
samtools - Utilities for the Sequence Alignment/Map (SAM) format
.B OPTIONS:
.RS
-.TP 8
+.TP 10
+.B -A
+Do not skip anomalous read pairs in variant calling.
+.TP
.B -B
Disable probabilistic realignment for the computation of base alignment
quality (BAQ). BAQ is the Phred-scaled probability of a read base being
about sqrt((INT-q)/INT)*INT. A zero value disables this
functionality; if enabled, the recommended value for BWA is 50. [0]
.TP
+.BI -d \ INT
+At a position, read maximally
+.I INT
+reads per input BAM. [250]
+.TP
+.B -D
+Output per-sample read depth
+.TP
.BI -e \ INT
Phred-scaled gap extension sequencing error probability. Reducing
.I INT
.IR INT * s / l .
[100]
.TP
+.B -I
+Do not perform INDEL calling
+.TP
.BI -l \ FILE
File containing a list of sites where pileup or BCF is outputted [null]
.TP
+.BI -L \ INT
+Skip INDEL calling if the average per-sample depth is above
+.IR INT .
+[250]
+.TP
.BI -o \ INT
Phred-scaled gap open sequencing error probability. Reducing
.I INT
.I STR
[all sites]
.TP
+.B -S
+Output per-sample Phred-scaled strand bias P-value
+.TP
.B -u
Similar to
.B -g
This command is much faster than replacing the header with a
BAM->SAM->BAM conversion.
+.TP
+.B cat
+samtools cat [-h header.sam] [-o out.bam] <in1.bam> <in2.bam> [ ... ]
+
+Concatenate BAMs. The sequence dictionary of each input BAM must be identical,
+although this command does not check this. This command uses a similar trick
+to
+.B reheader
+which enables fast BAM concatenation.
+
.TP
.B sort
samtools sort [-no] [-m maxMem] <in.bam> <out.prefix>
.TP
.B phase
-samtools phase [-F] [-k len] [-b prefix] [-q minLOD] [-Q minBaseQ] <in.bam>
+samtools phase [-AF] [-k len] [-b prefix] [-q minLOD] [-Q minBaseQ] <in.bam>
Call and phase heterozygous SNPs.
.B OPTIONS:
.RS
.TP 8
+.B -A
+Drop reads with ambiguous phase.
+.TP 8
.BI -b \ STR
Prefix of BAM output. When this option is in use, phase-0 reads will be saved in file
.BR STR .0.bam