X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=samtools.1;h=c71fc879d8c5f590f71a90cd27f09573b1520e62;hp=e0c77439751765b90aeb3c4ef50b8f4cb7d4a096;hb=9f4bebab2e0917c676ae739b2d05cb22ad6c4ed5;hpb=1539c893f863596db71ab2af75a802e935496940

diff --git a/samtools.1 b/samtools.1
index e0c7743..c71fc87 100644
--- 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
@@ -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>
@@ -253,7 +285,7 @@ Approximately the maximum required memory. [500000000]
 
 .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
@@ -270,6 +302,12 @@ and the headers of other files will be ignored.
 .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
@@ -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
+.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
+[null]
 .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