# Uploaded samtools version 0.1.14-1.

[samtools.git] / samtools.1

diff --git a/samtools.1 b/samtools.1
index e0595607196e577f15227c5cef8af0c9f51de2d6..ba323926d83451cf4013c511cf832d6e820a76f9 100644 (file)
--- a/samtools.1
+++ b/samtools.1
@@ -1,4 +1,4 @@
-.TH samtools 1 "21 November 2010" "samtools-0.1.11" "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
@@ -137,7 +137,7 @@ viewing the same reference sequence.
 
 .TP
 .B mpileup
-samtools mpileup [-Bug] [-C capQcoef] [-r reg] [-f in.fa] [-l list] [-M capMapQ] [-Q minBaseQ] [-q minMapQ] in.bam [in2.bam [...]]
+samtools mpileup [-EBug] [-C capQcoef] [-r reg] [-f in.fa] [-l list] [-M capMapQ] [-Q minBaseQ] [-q minMapQ] in.bam [in2.bam [...]]
 
 Generate BCF or pileup for one or multiple BAM files. Alignment records
 are grouped by sample identifiers in @RG header lines. If sample
@@ -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
@@ -159,11 +162,23 @@ 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
 leads to longer indels. [20]
 .TP
+.B -E
+Extended BAQ computation. This option helps sensitivity especially for MNPs, but may hurt
+specificity a little bit.
+.TP
 .BI -f \ FILE
 The reference file [null]
 .TP
@@ -180,9 +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
@@ -206,6 +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
@@ -223,6 +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>
@@ -355,7 +391,7 @@ Treat paired-end reads and single-end reads.
 
 .TP
 .B calmd
-samtools calmd [-eubSr] [-C capQcoef] <aln.bam> <ref.fasta>
+samtools calmd [-EeubSr] [-C capQcoef] <aln.bam> <ref.fasta>
 
 Generate the MD tag. If the MD tag is already present, this command will
 give a warning if the MD tag generated is different from the existing
@@ -388,7 +424,58 @@ Coefficient to cap mapping quality of poorly mapped reads. See the
 command for details. [0]
 .TP
 .B -r
-Compute the BQ tag without changing the base quality.
+Compute the BQ tag (without -A) or cap base quality by BAQ (with -A).
+.TP
+.B -E
+Extended BAQ calculation. This option trades specificity for sensitivity, though the
+effect is minor.
+.RE
+
+.TP
+.B targetcut
+samtools targetcut [-Q minBaseQ] [-i inPenalty] [-0 em0] [-1 em1] [-2 em2] [-f ref] <in.bam>
+
+This command identifies target regions by examining the continuity of read depth, computes
+haploid consensus sequences of targets and outputs a SAM with each sequence corresponding
+to a target. When option
+.B -f
+is in use, BAQ will be applied. This command is
+.B only
+designed for cutting fosmid clones from fosmid pool sequencing [Ref. Kitzman et al. (2010)].
+.RE
+
+.TP
+.B phase
+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
+and phase-1 reads in
+.BR 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
+.BR STR .chimeric.bam.
+[null]
+.TP
+.B -F
+Do not attempt to fix chimeric reads.
+.TP
+.BI -k \ INT
+Maximum length for local phasing. [13]
+.TP
+.BI -q \ INT
+Minimum Phred-scaled LOD to call a heterozygote. [40]
+.TP
+.BI -Q \ INT
+Minimum base quality to be used in het calling. [13]
 .RE
 
 .TP
@@ -629,6 +716,20 @@ mismatches. Applying this option usually helps
 .B BWA-short
 but may not other mappers.
 
+.IP o 2
+Generate the consensus sequence for one diploid individual:
+
+  samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq
+
+.IP o 2
+Phase one individual:
+
+  samtools calmd -AEur aln.bam ref.fa | samtools phase -b prefix - > phase.out
+
+The
+.B calmd
+command is used to reduce false heterozygotes around INDELs.
+
 .IP o 2
 Call SNPs and short indels for multiple diploid individuals: