1 .TH samtools 1 "6 July 2009" "samtools-0.1.5" "Bioinformatics tools"
4 samtools - Utilities for the Sequence Alignment/Map (SAM) format
7 samtools view -bt ref_list.txt -o aln.bam aln.sam.gz
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 Samtools is designed to work on a stream. It regards an input file `-'
31 as the standard input (stdin) and an output file `-' as the standard output
32 (stdout). Several commands can thus be combined with Unix pipes. Samtools
33 always output warning and error messages to the standard error output (stderr).
35 Samtools is also able to open a BAM (not SAM) file on a remote FTP server if the BAM
36 file name starts with `ftp://'.
37 Samtools checks the current working directory for the index file and will
38 download the index upon absence. Samtools achieves random FTP file access
39 with the `REST' ftp command. It does not retrieve the entire
40 alignment file unless it is asked to do so.
42 .SH COMMANDS AND OPTIONS
46 samtools import <in.ref_list> <in.sam> <out.bam>
48 Since 0.1.4, this command is an alias of:
50 samtools view -bt <in.ref_list> -o <out.bam> <in.sam>
54 samtools sort [-n] [-m maxMem] <in.bam> <out.prefix>
56 Sort alignments by leftmost coordinates. File
58 will be created. This command may also create temporary files
59 .I <out.prefix>.%d.bam
60 when the whole alignment cannot be fitted into memory (controlled by
67 Sort by read names rather than by chromosomal coordinates
70 Approximately the maximum required memory. [500000000]
75 samtools merge [-n] <out.bam> <in1.bam> <in2.bam> [...]
77 Merge multiple sorted alignments. The header of
81 and the headers of other files will be ignored.
87 The input alignments are sorted by read names rather than by chromosomal
93 samtools index <aln.bam>
95 Index sorted alignment for fast random access. Index file
101 samtools view [-bhuHS] [-t in.refList] [-o output] [-f reqFlag] [-F
102 skipFlag] [-q minMapQ] [-l library] [-r readGroup] <in.bam>|<in.sam> [region1 [...]]
104 Extract/print all or sub alignments in SAM or BAM format. If no region
105 is specified, all the alignments will be printed; otherwise only
106 alignments overlapping the specified regions will be output. An
107 alignment may be given multiple times if it is overlapping several
108 regions. A region can be presented, for example, in the following
109 format: `chr2', `chr2:1000000' or `chr2:1,000,000-2,000,000'. The coordinate
116 Output in the BAM format.
119 Output uncompressed BAM. This option saves time spent on compression/decomprssion
120 and is thus preferred when the output is piped to another samtools command.
123 Include the header in the output.
126 Output the header only.
129 Input is in SAM. If @SQ header lines are absent, the
134 This file is TAB-delimited. Each line must contain the reference name
135 and the length of the reference, one line for each distinct reference;
136 additional fields are ignored. This file also defines the order of the
137 reference sequences in sorting. If you run `samtools faidx <ref.fa>',
138 the resultant index file
148 Only output alignments with all bits in INT present in the FLAG
149 field. INT can be in hex in the format of /^0x[0-9A-F]+/ [0]
152 Skip alignments with bits present in INT [0]
155 Skip alignments with MAPQ smaller than INT [0]
158 Only output reads in library STR [null]
161 Only output reads in read group STR [null]
166 samtools faidx <ref.fasta> [region1 [...]]
168 Index reference sequence in the FASTA format or extract subsequence from
169 indexed reference sequence. If no region is specified,
171 will index the file and create
173 on the disk. If regions are speficified, the subsequences will be
174 retrieved and printed to stdout in the FASTA format. The input file can
181 samtools pileup [-f in.ref.fasta] [-t in.ref_list] [-l in.site_list]
182 [-iscgS2] [-T theta] [-N nHap] [-r pairDiffRate] <in.bam>|<in.sam>
184 Print the alignment in the pileup format. In the pileup format, each
185 line represents a genomic position, consisting of chromosome name,
186 coordinate, reference base, read bases, read qualities and alignment
187 mapping qualities. Information on match, mismatch, indel, strand,
188 mapping quality and start and end of a read are all encoded at the read
189 base column. At this column, a dot stands for a match to the reference
190 base on the forward strand, a comma for a match on the reverse strand,
191 `ACGTN' for a mismatch on the forward strand and `acgtn' for a mismatch
192 on the reverse strand. A pattern `\\+[0-9]+[ACGTNacgtn]+' indicates
193 there is an insertion between this reference position and the next
194 reference position. The length of the insertion is given by the integer
195 in the pattern, followed by the inserted sequence. Similarly, a pattern
196 `-[0-9]+[ACGTNacgtn]+' represents a deletion from the reference. The
197 deleted bases will be presented as `*' in the following lines. Also at
198 the read base column, a symbol `^' marks the start of a read segment
199 which is a contiguous subsequence on the read separated by `N/S/H' CIGAR
200 operations. The ASCII of the character following `^' minus 33 gives the
201 mapping quality. A symbol `$' marks the end of a read segment.
205 is applied, the consensus base, consensus quality, SNP quality and RMS
206 mapping quality of the reads covering the site will be inserted between
207 the `reference base' and the `read bases' columns. An indel occupies an
208 additional line. Each indel line consists of chromosome name,
209 coordinate, a star, the genotype, consensus quality, SNP quality, RMS
210 mapping quality, # covering reads, the first alllele, the second allele,
211 # reads supporting the first allele, # reads supporting the second
212 allele and # reads containing indels different from the top two alleles.
219 Print the mapping quality as the last column. This option makes the
220 output easier to parse, although this format is not space efficient.
224 The input file is in SAM.
228 Only output pileup lines containing indels.
232 The reference sequence in the FASTA format. Index file
239 Cap mapping quality at INT [60]
243 List of reference names ane sequence lengths, in the format described
246 command. If this option is present, samtools assumes the input
248 is in SAM format; otherwise it assumes in BAM format.
252 List of sites at which pileup is output. This file is space
253 delimited. The first two columns are required to be chromosome and
254 1-based coordinate. Additional columns are ignored. It is
255 recommended to use option
259 as in the default format we may not know the mapping quality.
263 Call the consensus sequence using MAQ consensus model. Options
269 are only effective when
277 Generate genotype likelihood in the binary GLFv3 format. This option
278 suppresses -c, -i and -s.
282 The theta parameter (error dependency coefficient) in the maq consensus
287 Number of haplotypes in the sample (>=2) [2]
291 Expected fraction of differences between a pair of haplotypes [0.001]
295 Phred probability of an indel in sequencing/prep. [40]
301 samtools tview <in.sorted.bam> [ref.fasta]
303 Text alignment viewer (based on the ncurses library). In the viewer,
304 press `?' for help and press `g' to check the alignment start from a
305 region in the format like `chr10:10,000,000'. Note that if the region
306 showed on the screen contains no mapped reads, a blank screen will be
307 seen. This is a known issue and will be improved later.
313 samtools fixmate <in.nameSrt.bam> <out.bam>
315 Fill in mate coordinates, ISIZE and mate related flags from a
316 name-sorted alignment.
320 samtools rmdup <input.srt.bam> <out.bam>
322 Remove potential PCR duplicates: if multiple read pairs have identical
323 external coordinates, only retain the pair with highest mapping quality.
326 works with FR orientation and requires ISIZE is correctly set.
332 samtools rmdupse <input.srt.bam> <out.bam>
334 Remove potential duplicates for single-ended reads. This command will
335 treat all reads as single-ended even if they are paired in fact.
341 samtools fillmd [-e] <aln.bam> <ref.fasta>
343 Generate the MD tag. If the MD tag is already present, this command will
344 give a warning if the MD tag generated is different from the existing
351 Convert a the read base to = if it is identical to the aligned reference
352 base. Indel caller does not support the = bases at the moment.
358 SAM is TAB-delimited. Apart from the header lines, which are started
359 with the `@' symbol, each alignment line consists of:
365 Col Field Description
367 1 QNAME Query (pair) NAME
369 3 RNAME Reference sequence NAME
370 4 POS 1-based leftmost POSition/coordinate of clipped sequence
371 5 MAPQ MAPping Quality (Phred-scaled)
372 6 CIAGR extended CIGAR string
373 7 MRNM Mate Reference sequence NaMe (`=' if same as RNAME)
374 8 MPOS 1-based Mate POSistion
375 9 ISIZE Inferred insert SIZE
376 10 SEQ query SEQuence on the same strand as the reference
377 11 QUAL query QUALity (ASCII-33 gives the Phred base quality)
378 12 OPT variable OPTional fields in the format TAG:VTYPE:VALUE
382 Each bit in the FLAG field is defined as:
390 0x0001 the read is paired in sequencing
391 0x0002 the read is mapped in a proper pair
392 0x0004 the query sequence itself is unmapped
393 0x0008 the mate is unmapped
394 0x0010 strand of the query (1 for reverse)
395 0x0020 strand of the mate
396 0x0040 the read is the first read in a pair
397 0x0080 the read is the second read in a pair
398 0x0100 the alignment is not primary
399 0x0200 the read fails platform/vendor quality checks
400 0x0400 the read is either a PCR or an optical duplicate
406 Unaligned words used in bam_import.c, bam_endian.h, bam.c and bam_aux.c.
408 CIGAR operation P is not properly handled at the moment.
412 Heng Li from the Sanger Institute wrote the C version of samtools. Bob
413 Handsaker from the Broad Institute implemented the BGZF library and Jue
414 Ruan from Beijing Genomics Institute wrote the RAZF library. Various
415 people in the 1000Genomes Project contributed to the SAM format
420 Samtools website: http://samtools.sourceforge.net
projects / samtools.git / blob