-.TH samtools 1 "15 April 2009" "samtools-0.1.3" "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
.SH SYNOPSIS
.PP
-samtools import ref_list.txt aln.sam.gz aln.bam
+samtools view -bt ref_list.txt -o aln.bam aln.sam.gz
.PP
samtools sort aln.bam aln.sorted
.PP
.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>
-Convert alignments in SAM format to BAM format. File
-.I <in.ref_list>
-is TAB-delimited. Each line must contain the reference name and the
-length of the reference, one line for each distinct reference;
-additional fields are ignored. This file also defines the order of the
-reference sequences in sorting. File
-.I <in.sam>
-can be optionally compressed by zlib or gzip. A single hyphen is
-recognized as stdin or stdout, depending on the context. If you run
-`samtools faidx <ref.fa>', the resultant index file
-.I <ref.fa>.fai
-can be used as this
-.I <in.ref_list>
-file.
+Since 0.1.4, this command is an alias of:
+
+samtools view -bt <in.ref_list> -o <out.bam> <in.sam>
.TP
.B sort
.TP
.B view
-samtools view [-bhH] <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
.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
.B -H
Output the header only.
+.TP
+.B -S
+Input is in SAM. If @SQ header lines are absent, the
+.B `-t'
+option is required.
+.TP
+.B -t FILE
+This file is TAB-delimited. Each line must contain the reference name
+and the length of the reference, one line for each distinct reference;
+additional fields are ignored. This file also defines the order of the
+reference sequences in sorting. If you run `samtools faidx <ref.fa>',
+the resultant index file
+.I <ref.fa>.fai
+can be used as this
+.I <in.ref_list>
+file.
+.TP
+.B -o FILE
+Output file [stdout]
+.TP
+.B -f INT
+Only output alignments with all bits in INT present in the FLAG
+field. INT can be in hex in the format of /^0x[0-9A-F]+/ [0]
+.TP
+.B -F INT
+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
.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,
there is an insertion between this reference position and the next
reference position. The length of the insertion is given by the integer
in the pattern, followed by the inserted sequence. Similarly, a pattern
-`-[0-9]+[ACGTNacgtn]+' represents a deletion from the reference. Also at
+`-[0-9]+[ACGTNacgtn]+' represents a deletion from the reference. The
+deleted bases will be presented as `*' in the following lines. Also at
the read base column, a symbol `^' marks the start of a read segment
which is a contiguous subsequence on the read separated by `N/S/H' CIGAR
operations. The ASCII of the character following `^' minus 33 gives the
If option
.B -c
-is applied, the consensus base, consensus quality, SNP quality and
-maximum mapping quality of the reads covering the site will be inserted
-between the `reference base' and the `read bases' columns. An indel
-occupies an additional line. Each indel line consists of chromosome
-name, coordinate, a star, top two high-scoring ins/del sequences, the
-number of alignments containing the first indel allele, the number of
-alignments containing the second indel allele, and the number of
-alignments containing indels different from the top two alleles.
+is applied, the consensus base, consensus quality, SNP quality and RMS
+mapping quality of the reads covering the site will be inserted between
+the `reference base' and the `read bases' columns. An indel occupies an
+additional line. Each indel line consists of chromosome name,
+coordinate, a star, the genotype, consensus quality, SNP quality, RMS
+mapping quality, # covering reads, the first alllele, the second allele,
+# reads supporting the first allele, # reads supporting the second
+allele and # reads containing indels different from the top two alleles.
.B OPTIONS:
.RS
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.
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
.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
.B -g
-Generate genotype likelihood in the binary GLFv2 format. This option
+Generate genotype likelihood in the binary GLFv3 format. This option
suppresses -c, -i and -s.
.TP
.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
.RE
+.TP
+.B rmdupse
+samtools rmdupse <input.srt.bam> <out.bam>
+
+Remove potential duplicates for single-ended reads. This command will
+treat all reads as single-ended even if they are paired in fact.
+
+.RE
+
+.TP
+.B fillmd
+samtools fillmd [-e] <aln.bam> <ref.fasta>
-.SH SAM FORFAM
+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
+tag.
+
+.B OPTIONS:
+.RS
+.TP 8
+.B -e
+Convert a the read base to = if it is identical to the aligned reference
+base. Indel caller does not support the = bases at the moment.
+
+.RE
+
+.SH SAM FORMAT
SAM is TAB-delimited. Apart from the header lines, which are started
with the `@' symbol, each alignment line consists of:
.SH LIMITATIONS
.PP
.IP o 2
-Reference sequence names and lengths are not acquired from the BAM/SAM header.
+Unaligned words used in bam_import.c, bam_endian.h, bam.c and bam_aux.c.
.IP o 2
CIGAR operation P is not properly handled at the moment.
-.IP o 2
-The text viewer mysteriously crashes in a very rare case.
.SH AUTHOR
.PP
projects / samtools.git / blobdiff