Uploaded samtools_0.1.16-1_amd64.changes.

[samtools.git] / samtools.1

diff --git a/samtools.1 b/samtools.1
index e0c77439751765b90aeb3c4ef50b8f4cb7d4a096..c71fc879d8c5f590f71a90cd27f09573b1520e62 100644 (file)
--- a/samtools.1
+++ b/samtools.1
@@ -1,4 +1,4 @@
-.TH samtools 1 "1 March 2011" "samtools-0.1.13" "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


@@ -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


@@ -159,6 +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
 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
 .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
 .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


@@ -210,6 +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


@@ -227,6 +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>


@@ -253,7 +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


@@ -270,6 +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


@@ -281,17 +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