Uploaded samtools_0.1.16-1_amd64.changes.

[samtools.git] / samtools.1

diff --git a/samtools.1 b/samtools.1
index e0595607196e577f15227c5cef8af0c9f51de2d6..c71fc879d8c5f590f71a90cd27f09573b1520e62 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 "21 April 2011" "samtools-0.1.16" "Bioinformatics tools"

 .SH NAME
 .PP
 samtools - Utilities for the Sequence Alignment/Map (SAM) format
 .SH NAME
 .PP
 samtools - Utilities for the Sequence Alignment/Map (SAM) format


@@ -137,7 +137,7 @@ viewing the same reference sequence.
 
 .TP
 .B mpileup
 
 .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
 
 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
 
 .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
 .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
 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
 .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
 .BI -f \ FILE
 The reference file [null]
 .TP


@@ -180,9 +195,17 @@ is modeled as
 .IR INT * s / l .
 [100]
 .TP
 .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 \ 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
 .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
 .I STR
 [all sites]
 .TP

+.B -S
+Output per-sample Phred-scaled strand bias P-value
+.TP

 .B -u
 Similar to
 .B -g
 .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.
 
 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 sort
 samtools sort [-no] [-m maxMem] <in.bam> <out.prefix>


@@ -249,7 +285,7 @@ Approximately the maximum required memory. [500000000]
 
 .TP
 .B merge
 
 .TP
 .B merge

-samtools merge [-nur] [-h inh.sam] [-R reg] <out.bam> <in1.bam> <in2.bam> [...]
+samtools merge [-nur1f] [-h inh.sam] [-R reg] <out.bam> <in1.bam> <in2.bam> [...]

 
 Merge multiple sorted alignments.
 The header reference lists of all the input BAM files, and the @SQ headers of
 
 Merge multiple sorted alignments.
 The header reference lists of all the input BAM files, and the @SQ headers of


@@ -266,6 +302,12 @@ and the headers of other files will be ignored.
 .B OPTIONS:
 .RS
 .TP 8
 .B OPTIONS:
 .RS
 .TP 8

+.B -1
+Use zlib compression level 1 to comrpess the output
+.TP
+.B -f
+Force to overwrite the output file if present.
+.TP 8

 .BI -h \ FILE
 Use the lines of
 .I FILE
 .BI -h \ FILE
 Use the lines of
 .I FILE


@@ -277,17 +319,18 @@ replacing any header lines that would otherwise be copied from
 is actually in SAM format, though any alignment records it may contain
 are ignored.)
 .TP
 is actually in SAM format, though any alignment records it may contain
 are ignored.)
 .TP

+.B -n
+The input alignments are sorted by read names rather than by chromosomal
+coordinates
+.TP

 .BI -R \ STR
 Merge files in the specified region indicated by
 .I STR
 .BI -R \ STR
 Merge files in the specified region indicated by
 .I STR

+[null]

 .TP
 .B -r
 Attach an RG tag to each alignment. The tag value is inferred from file names.
 .TP
 .TP
 .B -r
 Attach an RG tag to each alignment. The tag value is inferred from file names.
 .TP

-.B -n
-The input alignments are sorted by read names rather than by chromosomal
-coordinates
-.TP

 .B -u
 Uncompressed BAM output
 .RE
 .B -u
 Uncompressed BAM output
 .RE


@@ -355,7 +398,7 @@ Treat paired-end reads and single-end reads.
 
 .TP
 .B calmd
 
 .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
 
 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 +431,58 @@ Coefficient to cap mapping quality of poorly mapped reads. See the
 command for details. [0]
 .TP
 .B -r
 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
 .RE
 
 .TP


@@ -629,6 +723,20 @@ mismatches. Applying this option usually helps
 .B BWA-short
 but may not other mappers.
 
 .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:
 
 .IP o 2
 Call SNPs and short indels for multiple diploid individuals: