1 .TH samtools 1 "15 April 2009" "samtools-0.1.3" "Bioinformatics tools"
4 samtools - Utilities for the Sequence Alignment/Map (SAM) format
7 samtools import ref_list.txt aln.sam.gz aln.bam
9 samtools sort aln.bam aln.sorted
11 samtools index aln.sorted.bam
13 samtools view aln.sorted.bam chr2:20,100,000-20,200,000
15 samtools merge out.bam in1.bam in2.bam in3.bam
17 samtools faidx ref.fasta
19 samtools pileup -f ref.fasta aln.sorted.bam
21 samtools tview aln.sorted.bam ref.fasta
25 Samtools is a set of utilities that manipulate alignments in the BAM
26 format. It imports from and exports to the SAM (Sequence
27 Alignment/Map) format, does sorting, merging and indexing, and
28 allows to retrieve reads in any regions swiftly.
30 .SH COMMANDS AND OPTIONS
33 samtools import <in.ref_list> <in.sam> <out.bam>
35 Convert alignments in SAM format to BAM format. File
37 is TAB-delimited. Each line must contain the reference name and the
38 length of the reference, one line for each distinct reference;
39 additional fields are ignored. This file also defines the order of the
40 reference sequences in sorting. File
42 can be optionally compressed by zlib or gzip. A single hyphen is
43 recognized as stdin or stdout, depending on the context. If you run
44 `samtools faidx <ref.fa>', the resultant index file
52 samtools sort [-n] [-m maxMem] <in.bam> <out.prefix>
54 Sort alignments by leftmost coordinates. File
56 will be created. This command may also create temporary files
57 .I <out.prefix>.%d.bam
58 when the whole alignment cannot be fitted into memory (controlled by
65 Sort by read names rather than by chromosomal coordinates
68 Approximately the maximum required memory. [500000000]
73 samtools merge [-n] <out.bam> <in1.bam> <in2.bam> [...]
75 Merge multiple sorted alignments. The header of
79 and the headers of other files will be ignored.
85 The input alignments are sorted by read names rather than by chromosomal
91 samtools index <aln.bam>
93 Index sorted alignment for fast random access. Index file
99 samtools view [-bhH] <in.bam> [region1 [...]]
101 Extract/print all or sub alignments in SAM or BAM format. If no region
102 is specified, all the alignments will be printed; otherwise only
103 alignments overlapping with the specified regions will be output. An
104 alignment may be given multiple times if it is overlapping several
105 regions. A region can be presented, for example, in the following
106 format: `chr2', `chr2:1000000' or `chr2:1,000,000-2,000,000'.
112 Output in the BAM format.
115 Include the header in the output.
118 Output the header only.
123 samtools faidx <ref.fasta> [region1 [...]]
125 Index reference sequence in the FASTA format or extract subsequence from
126 indexed reference sequence. If no region is specified,
128 will index the file and create
130 on the disk. If regions are speficified, the subsequences will be
131 retrieved and printed to stdout in the FASTA format. The input file can
138 samtools pileup [-f in.ref.fasta] [-t in.ref_list] [-l in.site_list]
139 [-iscg] [-T theta] [-N nHap] [-r pairDiffRate] <in.alignment>
141 Print the alignment in the pileup format. In the pileup format, each
142 line represents a genomic position, consisting of chromosome name,
143 coordinate, reference base, read bases, read qualities and alignment
144 mapping qualities. Information on match, mismatch, indel, strand,
145 mapping quality and start and end of a read are all encoded at the read
146 base column. At this column, a dot stands for a match to the reference
147 base on the forward strand, a comma for a match on the reverse strand,
148 `ACGTN' for a mismatch on the forward strand and `acgtn' for a mismatch
149 on the reverse strand. A pattern `\\+[0-9]+[ACGTNacgtn]+' indicates
150 there is an insertion between this reference position and the next
151 reference position. The length of the insertion is given by the integer
152 in the pattern, followed by the inserted sequence. Similarly, a pattern
153 `-[0-9]+[ACGTNacgtn]+' represents a deletion from the reference. Also at
154 the read base column, a symbol `^' marks the start of a read segment
155 which is a contiguous subsequence on the read separated by `N/S/H' CIGAR
156 operations. The ASCII of the character following `^' minus 33 gives the
157 mapping quality. A symbol `$' marks the end of a read segment.
161 is applied, the consensus base, consensus quality, SNP quality and
162 maximum mapping quality of the reads covering the site will be inserted
163 between the `reference base' and the `read bases' columns. An indel
164 occupies an additional line. Each indel line consists of chromosome
165 name, coordinate, a star, top two high-scoring ins/del sequences, the
166 number of alignments containing the first indel allele, the number of
167 alignments containing the second indel allele, and the number of
168 alignments containing indels different from the top two alleles.
175 Print the mapping quality as the last column. This option makes the
176 output easier to parse, although this format is not space efficient.
180 Only output pileup lines containing indels.
184 The reference sequence in the FASTA format. Index file
191 List of reference names ane sequence lengths, in the format described
194 command. If this option is present, samtools assumes the input
196 is in SAM format; otherwise it assumes in BAM format.
200 List of sites at which pileup is output. This file is space
201 delimited. The first two columns are required to be chromosome and
202 1-based coordinate. Additional columns are ignored. It is
203 recommended to use option
207 as in the default format we may not know the mapping quality.
211 Call the consensus sequence using MAQ consensus model. Options
216 are only effective when
222 Generate genotype likelihood in the binary GLFv2 format. This option
223 suppresses -c, -i and -s.
227 The theta parameter (error dependency coefficient) in the maq consensus
232 Number of haplotypes in the sample (>=2) [2]
236 Expected fraction of differences between a pair of haplotypes [0.001]
242 samtools tview <in.sorted.bam> [ref.fasta]
244 Text alignment viewer (based on the ncurses library). In the viewer,
245 press `?' for help and press `g' to check the alignment start from a
246 region in the format like `chr10:10,000,000'. Note that if the region
247 showed on the screen contains no mapped reads, a blank screen will be
248 seen. This is a known issue and will be improved later.
254 samtools fixmate <in.nameSrt.bam> <out.bam>
256 Fill in mate coordinates, ISIZE and mate related flags from a
257 name-sorted alignment.
261 samtools rmdup <input.srt.bam> <out.bam>
263 Remove potential PCR duplicates: if multiple read pairs have identical
264 external coordinates, only retain the pair with highest mapping quality.
267 works with FR orientation and requires ISIZE is correctly set.
274 SAM is TAB-delimited. Apart from the header lines, which are started
275 with the `@' symbol, each alignment line consists of:
281 Col Field Description
283 1 QNAME Query (pair) NAME
285 3 RNAME Reference sequence NAME
286 4 POS 1-based leftmost POSition/coordinate of clipped sequence
287 5 MAPQ MAPping Quality (Phred-scaled)
288 6 CIAGR extended CIGAR string
289 7 MRNM Mate Reference sequence NaMe (`=' if same as RNAME)
290 8 MPOS 1-based Mate POSistion
291 9 ISIZE Inferred insert SIZE
292 10 SEQ query SEQuence on the same strand as the reference
293 11 QUAL query QUALity (ASCII-33 gives the Phred base quality)
294 12 OPT variable OPTional fields in the format TAG:VTYPE:VALUE
298 Each bit in the FLAG field is defined as:
306 0x0001 the read is paired in sequencing
307 0x0002 the read is mapped in a proper pair
308 0x0004 the query sequence itself is unmapped
309 0x0008 the mate is unmapped
310 0x0010 strand of the query (1 for reverse)
311 0x0020 strand of the mate
312 0x0040 the read is the first read in a pair
313 0x0080 the read is the second read in a pair
314 0x0100 the alignment is not primary
315 0x0200 the read fails platform/vendor quality checks
316 0x0400 the read is either a PCR or an optical duplicate
322 Reference sequence names and lengths are not acquired from the BAM/SAM header.
324 CIGAR operation P is not properly handled at the moment.
326 The text viewer mysteriously crashes in a very rare case.
330 Heng Li from the Sanger Institute wrote the C version of samtools. Bob
331 Handsaker from the Broad Institute implemented the BGZF library and Jue
332 Ruan from Beijing Genomics Institute wrote the RAZF library. Various
333 people in the 1000Genomes Project contributed to the SAM format
338 Samtools website: http://samtools.sourceforge.net
projects / samtools.git / blob