-.TH samtools 1 "22 December 2008" "samtools-0.1.1" "Bioinformatics tools"
+.TH samtools 1 "15 April 2009" "samtools-0.1.3" "Bioinformatics tools"
.SH NAME
.PP
samtools - Utilities for the Sequence Alignment/Map (SAM) format
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.
+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.
.TP
.B sort
samtools sort [-n] [-m maxMem] <in.bam> <out.prefix>
-Sort alignments based on the leftmost coordinate. File
+Sort alignments by leftmost coordinates. File
.I <out.prefix>.bam
will be created. This command may also create temporary files
.I <out.prefix>.%d.bam
Sort by read names rather than by chromosomal coordinates
.TP
.B -m INT
-Approximately the maximum required memory.
+Approximately the maximum required memory. [500000000]
.RE
.TP
.TP
.B view
-samtools view [-b] <in.bam> [region1 [...]]
+samtools view [-bhH] <in.bam> [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
.TP 8
.B -b
Output in the BAM format.
+.TP
+.B -h
+Include the header in the output.
+.TP
+.B -H
+Output the header only.
.RE
.TP
.TP
.B pileup
samtools pileup [-f in.ref.fasta] [-t in.ref_list] [-l in.site_list]
-[-s] [-c] [-T theta] [-N nHap] [-r pairDiffRate] <in.alignment>
+[-iscg] [-T theta] [-N nHap] [-r pairDiffRate] <in.alignment>
Print the alignment in the pileup format. In the pileup format, each
line represents a genomic position, consisting of chromosome name,
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 reads strongly supporting the first indel, the number of reads
-strongly supporting the second indel, the number of reads that confer
-little information on distinguishing indels and the number of reads that
-contain indels different from the top two ones.
+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.
.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 -i
+Only output pileup lines containing indels.
+
.TP
.B -f FILE
The reference sequence in the FASTA format. Index file
.TP
.B -c
-Call the consensus sequnce using MAQ consensus model. Options
+Call the consensus sequence using MAQ consensus model. Options
.B -T,
.B -N
and
.B -c
is in use.
+.TP
+.B -g
+Generate genotype likelihood in the binary GLFv2 format. This option
+suppresses -c, -i and -s.
+
.TP
.B -T FLOAT
The theta parameter (error dependency coefficient) in the maq consensus
.RE
+.TP
+.B fixmate
+samtools fixmate <in.nameSrt.bam> <out.bam>
+
+Fill in mate coordinates, ISIZE and mate related flags from a
+name-sorted alignment.
+
+.TP
+.B rmdup
+samtools rmdup <input.srt.bam> <out.bam>
+
+Remove potential PCR duplicates: if multiple read pairs have identical
+external coordinates, only retain the pair with highest mapping quality.
+This command
+.B ONLY
+works with FR orientation and requires ISIZE is correctly set.
+
+.RE
+
+
+.SH SAM FORFAM
+
+SAM is TAB-delimited. Apart from the header lines, which are started
+with the `@' symbol, each alignment line consists of:
+
+.TS
+center box;
+cb | cb | cb
+n | l | l .
+Col Field Description
+_
+1 QNAME Query (pair) NAME
+2 FLAG bitwise FLAG
+3 RNAME Reference sequence NAME
+4 POS 1-based leftmost POSition/coordinate of clipped sequence
+5 MAPQ MAPping Quality (Phred-scaled)
+6 CIAGR extended CIGAR string
+7 MRNM Mate Reference sequence NaMe (`=' if same as RNAME)
+8 MPOS 1-based Mate POSistion
+9 ISIZE Inferred insert SIZE
+10 SEQ query SEQuence on the same strand as the reference
+11 QUAL query QUALity (ASCII-33 gives the Phred base quality)
+12 OPT variable OPTional fields in the format TAG:VTYPE:VALUE
+.TE
+
+.PP
+Each bit in the FLAG field is defined as:
+
+.TS
+center box;
+cb | cb
+l | l .
+Flag Description
+_
+0x0001 the read is paired in sequencing
+0x0002 the read is mapped in a proper pair
+0x0004 the query sequence itself is unmapped
+0x0008 the mate is unmapped
+0x0010 strand of the query (1 for reverse)
+0x0020 strand of the mate
+0x0040 the read is the first read in a pair
+0x0080 the read is the second read in a pair
+0x0100 the alignment is not primary
+0x0200 the read fails platform/vendor quality checks
+0x0400 the read is either a PCR or an optical duplicate
+.TE
+
.SH LIMITATIONS
.PP
.IP o 2
-In general, more testing is needed to ensure there is no severe bug.
-.IP o 2
-PCR duplicate removal has not been implemented.
-.IP o 2
-Only MAQ->SAM converter is implemented. More converters are needed.
-.IP o 2
Reference sequence names and lengths are not acquired from the BAM/SAM header.
.IP o 2
-CIGAR operations N and P may not be properly handled.
+CIGAR operation P is not properly handled at the moment.
.IP o 2
-There is a small known memory leak in the viewer.
+The text viewer mysteriously crashes in a very rare case.
.SH AUTHOR
.PP
-Heng Li from the Sanger Institute is the author of samtools. Bob
+Heng Li from the Sanger Institute wrote the C version of samtools. Bob
Handsaker from the Broad Institute implemented the BGZF library and Jue
Ruan from Beijing Genomics Institute wrote the RAZF library. Various
people in the 1000Genomes Project contributed to the SAM format
projects / samtools.git / blobdiff