* samtools-0.1.5-7 (r403)

[samtools.git] / samtools.1

diff --git a/samtools.1 b/samtools.1
index c4bd77e3e53ca2c26d0bbf58e638105037d79ab2..11ea5b66bb72e15e1789328bde3783ada21b958b 100644 (file)
--- a/samtools.1
+++ b/samtools.1
@@ -1,4 +1,4 @@
-.TH samtools 1 "21 May 2009" "samtools-0.1.4" "Bioinformatics tools"
+.TH samtools 1 "6 July 2009" "samtools-0.1.5" "Bioinformatics tools"
 .SH NAME
 .PP
 samtools - Utilities for the Sequence Alignment/Map (SAM) format
@@ -23,11 +23,25 @@ samtools tview aln.sorted.bam ref.fasta
 .SH DESCRIPTION
 .PP
 Samtools is a set of utilities that manipulate alignments in the BAM
-format. It imports from and exports to the SAM (Sequence
-Alignment/Map) format, does sorting, merging and indexing, and
-allows to retrieve reads in any regions swiftly.
+format. It imports from and exports to the SAM (Sequence Alignment/Map)
+format, does sorting, merging and indexing, and allows to retrieve reads
+in any regions swiftly.
+
+Samtools is designed to work on a stream. It regards an input file `-'
+as the standard input (stdin) and an output file `-' as the standard
+output (stdout). Several commands can thus be combined with Unix
+pipes. Samtools always output warning and error messages to the standard
+error output (stderr).
+
+Samtools is also able to open a BAM (not SAM) file on a remote FTP
+server if the BAM file name starts with `ftp://'.  Samtools checks the
+current working directory for the index file and will download the index
+upon absence. Samtools achieves random FTP file access with the `REST'
+ftp command. It does not retrieve the entire alignment file unless it is
+asked to do so.
 
 .SH COMMANDS AND OPTIONS
+
 .TP 10
 .B import
 samtools import <in.ref_list> <in.sam> <out.bam>
@@ -85,15 +99,16 @@ will be created.
 
 .TP
 .B view
-samtools view [-bhHS] [-t in.refList] [-o output] [-f reqFlag] [-F
-skipFlag] [-q minMapQ] <in.bam> [region1 [...]]
+samtools view [-bhuHS] [-t in.refList] [-o output] [-f reqFlag] [-F
+skipFlag] [-q minMapQ] [-l library] [-r readGroup] <in.bam>|<in.sam> [region1 [...]]
 
 Extract/print all or sub alignments in SAM or BAM format. If no region
 is specified, all the alignments will be printed; otherwise only
-alignments overlapping with the specified regions will be output. An
+alignments overlapping the specified regions will be output. An
 alignment may be given multiple times if it is overlapping several
 regions. A region can be presented, for example, in the following
-format: `chr2', `chr2:1000000' or `chr2:1,000,000-2,000,000'.
+format: `chr2', `chr2:1000000' or `chr2:1,000,000-2,000,000'. The
+coordinate is 1-based.
 
 .B OPTIONS:
 .RS
@@ -101,6 +116,11 @@ format: `chr2', `chr2:1000000' or `chr2:1,000,000-2,000,000'.
 .B -b
 Output in the BAM format.
 .TP
+.B -u
+Output uncompressed BAM. This option saves time spent on
+compression/decomprssion and is thus preferred when the output is piped
+to another samtools command.
+.TP
 .B -h
 Include the header in the output.
 .TP
@@ -135,6 +155,12 @@ Skip alignments with bits present in INT [0]
 .TP
 .B -q INT
 Skip alignments with MAPQ smaller than INT [0]
+.TP
+.B -l STR
+Only output reads in library STR [null]
+.TP
+.B -r STR
+Only output reads in read group STR [null]
 .RE
 
 .TP
@@ -155,7 +181,7 @@ format.
 .TP
 .B pileup
 samtools pileup [-f in.ref.fasta] [-t in.ref_list] [-l in.site_list]
-[-iscg] [-T theta] [-N nHap] [-r pairDiffRate] <in.alignment>
+[-iscgS2] [-T theta] [-N nHap] [-r pairDiffRate] <in.bam>|<in.sam>
 
 Print the alignment in the pileup format. In the pileup format, each
 line represents a genomic position, consisting of chromosome name,
@@ -195,6 +221,10 @@ allele and # reads containing indels different from the top two alleles.
 Print the mapping quality as the last column. This option makes the
 output easier to parse, although this format is not space efficient.
 
+.TP
+.B -S
+The input file is in SAM.
+
 .TP
 .B -i
 Only output pileup lines containing indels.
@@ -206,6 +236,10 @@ The reference sequence in the FASTA format. Index file
 will be created if
 absent.
 
+.TP
+.B -M INT
+Cap mapping quality at INT [60]
+
 .TP
 .B -t FILE
 List of reference names ane sequence lengths, in the format described
@@ -230,11 +264,14 @@ as in the default format we may not know the mapping quality.
 .B -c
 Call the consensus sequence using MAQ consensus model. Options
 .B -T,
-.B -N
+.B -N,
+.B -I
 and
 .B -r
 are only effective when
 .B -c
+or
+.B -g
 is in use.
 
 .TP
@@ -255,6 +292,10 @@ Number of haplotypes in the sample (>=2) [2]
 .B -r FLOAT
 Expected fraction of differences between a pair of haplotypes [0.001]
 
+.TP
+.B -I INT
+Phred probability of an indel in sequencing/prep. [40]
+
 .RE
 
 .TP
@@ -263,9 +304,7 @@ samtools tview <in.sorted.bam> [ref.fasta]
 
 Text alignment viewer (based on the ncurses library). In the viewer,
 press `?' for help and press `g' to check the alignment start from a
-region in the format like `chr10:10,000,000'. Note that if the region
-showed on the screen contains no mapped reads, a blank screen will be
-seen. This is a known issue and will be improved later.
+region in the format like `chr10:10,000,000'.
 
 .RE
 
@@ -314,8 +353,7 @@ base. Indel caller does not support the = bases at the moment.
 
 .RE
 
-
-.SH SAM FORFAM
+.SH SAM FORMAT
 
 SAM is TAB-delimited. Apart from the header lines, which are started
 with the `@' symbol, each alignment line consists of: