Release samtools-0.1.14 (r933:170)

[samtools.git] / samtools.1

diff --git a/samtools.1 b/samtools.1
index 8d299b78dc079b6961e14137324ecad32e4b66d0..ba323926d83451cf4013c511cf832d6e820a76f9 100644 (file)
--- a/samtools.1
+++ b/samtools.1
@@ -1,4 +1,4 @@
-.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
@@ -145,7 +145,10 @@ identifiers are absent, each input file is regarded as one sample.
 
 .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
@@ -159,6 +162,14 @@ being generated from the mapped position, the new mapping quality is
 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
@@ -184,9 +195,17 @@ is modeled as
 .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
@@ -210,6 +229,9 @@ Only generate pileup in region
 .I STR
 [all sites]
 .TP
+.B -S
+Output per-sample Phred-scaled strand bias P-value
+.TP
 .B -u
 Similar to
 .B -g
@@ -227,6 +249,16 @@ with the header in
 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>
@@ -414,12 +446,15 @@ designed for cutting fosmid clones from fosmid pool sequencing [Ref. Kitzman et
 
 .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