samtools index aln.sorted.bam
+ samtools idxstats aln.sorted.bam
+
samtools view aln.sorted.bam chr2:20,100,000-20,200,000
samtools merge out.bam in1.bam in2.bam in3.bam
samtools pileup -f ref.fasta aln.sorted.bam
+ samtools mpileup -f ref.fasta -r chr3:1,000-2,000 in1.bam in2.bam
+
samtools tview aln.sorted.bam ref.fasta
COMMANDS AND OPTIONS
- import samtools import <in.ref_list> <in.sam> <out.bam>
-
- Since 0.1.4, this command is an alias of:
-
- samtools view -bt <in.ref_list> -o <out.bam> <in.sam>
-
-
- sort samtools sort [-n] [-m maxMem] <in.bam> <out.prefix>
-
- Sort alignments by leftmost coordinates. File <out.pre-
- fix>.bam will be created. This command may also create tempo-
- rary files <out.prefix>.%d.bam when the whole alignment can-
- not be fitted into memory (controlled by option -m).
-
- OPTIONS:
-
- -n Sort by read names rather than by chromosomal coordi-
- nates
-
- -m INT Approximately the maximum required memory.
- [500000000]
-
-
- merge samtools merge [-h inh.sam] [-n] <out.bam> <in1.bam>
- <in2.bam> [...]
-
- Merge multiple sorted alignments. The header reference lists
- of all the input BAM files, and the @SQ headers of inh.sam,
- if any, must all refer to the same set of reference
- sequences. The header reference list and (unless overridden
- by -h) `@' headers of in1.bam will be copied to out.bam, and
- the headers of other files will be ignored.
-
- OPTIONS:
-
- -h FILE Use the lines of FILE as `@' headers to be copied to
- out.bam, replacing any header lines that would other-
- wise be copied from in1.bam. (FILE is actually in
- SAM format, though any alignment records it may con-
- tain are ignored.)
-
- -n The input alignments are sorted by read names rather
- than by chromosomal coordinates
-
-
- index samtools index <aln.bam>
-
- Index sorted alignment for fast random access. Index file
- <aln.bam>.bai will be created.
-
-
view samtools view [-bhuHS] [-t in.refList] [-o output] [-f
- reqFlag] [-F skipFlag] [-q minMapQ] [-l library] [-r read-
- Group] <in.bam>|<in.sam> [region1 [...]]
+ reqFlag] [-F skipFlag] [-q minMapQ] [-l library] [-r read-
+ Group] [-R rgFile] <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 the specified regions
- will be output. An alignment may be given multiple times if
+ 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 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' (the whole
- chr2), `chr2:1000000' (region starting from 1,000,000bp) or
- `chr2:1,000,000-2,000,000' (region between 1,000,000 and
- 2,000,000bp including the end points). The coordinate is
+ for example, in the following format: `chr2' (the whole
+ chr2), `chr2:1000000' (region starting from 1,000,000bp) or
+ `chr2:1,000,000-2,000,000' (region between 1,000,000 and
+ 2,000,000bp including the end points). The coordinate is
1-based.
OPTIONS:
-b Output in the BAM format.
-u Output uncompressed BAM. This option saves time spent
- on compression/decomprssion and is thus preferred
+ on compression/decomprssion and is thus preferred
when the output is piped to another samtools command.
-h Include the header in the output.
-H Output the header only.
- -S Input is in SAM. If @SQ header lines are absent, the
+ -S Input is in SAM. If @SQ header lines are absent, the
`-t' option is required.
- -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
- <ref.fa>.fai can be used as this <in.ref_list> file.
+ -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
+ <ref.fa>.fai can be used as this <in.ref_list> file.
-o FILE Output file [stdout]
- -f INT Only output alignments with all bits in INT present
+ -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]
-r STR Only output reads in read group STR [null]
+ -R FILE Output reads in read groups listed in FILE [null]
- faidx samtools faidx <ref.fasta> [region1 [...]]
- Index reference sequence in the FASTA format or extract sub-
- sequence from indexed reference sequence. If no region is
- specified, faidx will index the file and create
- <ref.fasta>.fai on the disk. If regions are speficified, the
- subsequences will be retrieved and printed to stdout in the
- FASTA format. The input file can be compressed in the RAZF
- format.
+ tview 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 align-
+ ment start from a region in the format like
+ `chr10:10,000,000' or `=10,000,000' when viewing the same
+ reference sequence.
- pileup samtools pileup [-f in.ref.fasta] [-t in.ref_list] [-l
- in.site_list] [-iscgS2] [-T theta] [-N nHap] [-r
+ pileup samtools pileup [-f in.ref.fasta] [-t in.ref_list] [-l
+ in.site_list] [-iscgS2] [-T theta] [-N nHap] [-r
pairDiffRate] <in.bam>|<in.sam>
- Print the alignment in the pileup format. In the pileup for-
- mat, each line represents a genomic position, consisting of
+ Print the alignment in the pileup format. In the pileup for-
+ mat, each line represents a genomic position, consisting of
chromosome name, coordinate, reference base, read bases, read
- qualities and alignment mapping qualities. Information on
+ qualities and alignment mapping qualities. Information on
match, mismatch, indel, strand, mapping quality and start and
- end of a read are all encoded at the read base column. At
- this column, a dot stands for a match to the reference base
- on the forward strand, a comma for a match on the reverse
- strand, `ACGTN' for a mismatch on the forward strand and
- `acgtn' for a mismatch on the reverse strand. A pattern
- `\+[0-9]+[ACGTNacgtn]+' indicates there is an insertion
- between this reference position and the next reference posi-
- tion. The length of the insertion is given by the integer in
- the pattern, followed by the inserted sequence. Similarly, a
+ end of a read are all encoded at the read base column. At
+ this column, a dot stands for a match to the reference base
+ on the forward strand, a comma for a match on the reverse
+ strand, `ACGTN' for a mismatch on the forward strand and
+ `acgtn' for a mismatch on the reverse strand. A pattern
+ `\+[0-9]+[ACGTNacgtn]+' indicates there is an insertion
+ between this reference position and the next reference posi-
+ tion. 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. 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 sub-
- sequence on the read separated by `N/S/H' CIGAR operations.
- The ASCII of the character following `^' minus 33 gives the
- mapping quality. A symbol `$' marks the end of a read seg-
+ reference. The deleted bases will be presented as `*' in the
+ following lines. Also at the read base column, a symbol `^'
+ marks the start of a read segment which is a contiguous sub-
+ sequence on the read separated by `N/S/H' CIGAR operations.
+ The ASCII of the character following `^' minus 33 gives the
+ mapping quality. A symbol `$' marks the end of a read seg-
ment.
- If option -c is applied, the consensus base, Phred-scaled
- consensus quality, SNP quality (i.e. the Phred-scaled proba-
+ If option -c is applied, the consensus base, Phred-scaled
+ consensus quality, SNP quality (i.e. the Phred-scaled proba-
bility of the consensus being identical to the reference) and
- root mean square (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, coordi-
- nate, a star, the genotype, consensus quality, SNP quality,
+ root mean square (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, coordi-
+ nate, 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
+ second allele, # reads supporting the first allele, # reads
+ supporting the second allele and # reads containing indels
different from the top two alleles.
- OPTIONS:
+ The position of indels is offset by -1.
+ OPTIONS:
- -s Print the mapping quality as the last column. This
- option makes the output easier to parse, although
+ -s Print the mapping quality as the last column. This
+ option makes the output easier to parse, although
this format is not space efficient.
-
-S The input file is in SAM.
-
-i Only output pileup lines containing indels.
-
- -f FILE The reference sequence in the FASTA format. Index
+ -f FILE The reference sequence in the FASTA format. Index
file FILE.fai will be created if absent.
-
-M INT Cap mapping quality at INT [60]
+ -m INT Filter reads with flag containing bits in INT
+ [1796]
- -t FILE List of reference names ane sequence lengths, in
- the format described for the import command. If
- this option is present, samtools assumes the input
+ -d INT Use the first NUM reads in the pileup for indel
+ calling for speed up. Zero for unlimited. [0]
+
+ -t FILE List of reference names ane sequence lengths, in
+ the format described for the import command. If
+ this option is present, samtools assumes the input
<in.alignment> is in SAM format; otherwise it
assumes in BAM format.
-
- -l FILE List of sites at which pileup is output. This file
- is space delimited. The first two columns are
- required to be chromosome and 1-based coordinate.
- Additional columns are ignored. It is recommended
+ -l FILE List of sites at which pileup is output. This file
+ is space delimited. The first two columns are
+ required to be chromosome and 1-based coordinate.
+ Additional columns are ignored. It is recommended
to use option -s together with -l as in the default
format we may not know the mapping quality.
-
- -c Call the consensus sequence using MAQ consensus
+ -c Call the consensus sequence using SOAPsnp consensus
model. Options -T, -N, -I and -r are only effective
when -c or -g is in use.
-
- -g Generate genotype likelihood in the binary GLFv3
+ -g Generate genotype likelihood in the binary GLFv3
format. This option suppresses -c, -i and -s.
-
- -T FLOAT The theta parameter (error dependency coefficient)
+ -T FLOAT The theta parameter (error dependency coefficient)
in the maq consensus calling model [0.85]
-
-N INT Number of haplotypes in the sample (>=2) [2]
-
- -r FLOAT Expected fraction of differences between a pair of
+ -r FLOAT Expected fraction of differences between a pair of
haplotypes [0.001]
-
- -I INT Phred probability of an indel in sequencing/prep.
+ -I INT Phred probability of an indel in sequencing/prep.
[40]
+ mpileup samtools mpileup [-r reg] [-f in.fa] in.bam [in2.bam [...]]
- tview samtools tview <in.sorted.bam> [ref.fasta]
+ Generate pileup for multiple BAM files. Consensus calling is
+ not implemented.
+
+ OPTIONS:
+
+ -r STR Only generate pileup in region STR [all sites]
+
+ -f FILE The reference file [null]
+
+
+ reheader samtools reheader <in.header.sam> <in.bam>
+
+ Replace the header in in.bam with the header in
+ in.header.sam. This command is much faster than replacing
+ the header with a BAM->SAM->BAM conversion.
+
+
+ sort samtools sort [-no] [-m maxMem] <in.bam> <out.prefix>
+
+ Sort alignments by leftmost coordinates. File <out.pre-
+ fix>.bam will be created. This command may also create tempo-
+ rary files <out.prefix>.%d.bam when the whole alignment can-
+ not be fitted into memory (controlled by option -m).
+
+ OPTIONS:
+
+ -o Output the final alignment to the standard output.
+
+ -n Sort by read names rather than by chromosomal coordi-
+ nates
+
+ -m INT Approximately the maximum required memory.
+ [500000000]
+
+
+ merge samtools merge [-h inh.sam] [-nr] <out.bam> <in1.bam>
+ <in2.bam> [...]
+
+ Merge multiple sorted alignments. The header reference lists
+ of all the input BAM files, and the @SQ headers of inh.sam,
+ if any, must all refer to the same set of reference
+ sequences. The header reference list and (unless overridden
+ by -h) `@' headers of in1.bam will be copied to out.bam, and
+ the headers of other files will be ignored.
+
+ OPTIONS:
+
+ -h FILE Use the lines of FILE as `@' headers to be copied to
+ out.bam, replacing any header lines that would other-
+ wise be copied from in1.bam. (FILE is actually in
+ SAM format, though any alignment records it may con-
+ tain are ignored.)
+
+ -r Attach an RG tag to each alignment. The tag value is
+ inferred from file names.
+
+ -n The input alignments are sorted by read names rather
+ than by chromosomal coordinates
+
+
+ index samtools index <aln.bam>
+
+ Index sorted alignment for fast random access. Index file
+ <aln.bam>.bai will be created.
+
+
+ idxstats samtools idxstats <aln.bam>
- Text alignment viewer (based on the ncurses library). In the
- viewer, press `?' for help and press `g' to check the align-
- ment start from a region in the format like
- `chr10:10,000,000'.
+ Retrieve and print stats in the index file. The output is TAB
+ delimited with each line consisting of reference sequence
+ name, sequence length, # mapped reads and # unmapped reads.
+
+
+ faidx samtools faidx <ref.fasta> [region1 [...]]
+
+ Index reference sequence in the FASTA format or extract sub-
+ sequence from indexed reference sequence. If no region is
+ specified, faidx will index the file and create
+ <ref.fasta>.fai on the disk. If regions are speficified, the
+ subsequences will be retrieved and printed to stdout in the
+ FASTA format. The input file can be compressed in the RAZF
+ format.
fixmate samtools fixmate <in.nameSrt.bam> <out.bam>
name-sorted alignment.
- rmdup samtools rmdup <input.srt.bam> <out.bam>
+ rmdup samtools rmdup [-sS] <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 ONLY works with FR
- orientation and requires ISIZE is correctly set.
+ Remove potential PCR duplicates: if multiple read pairs have
+ identical external coordinates, only retain the pair with
+ highest mapping quality. In the paired-end mode, this com-
+ mand ONLY works with FR orientation and requires ISIZE is
+ correctly set. It does not work for unpaired reads (e.g. two
+ ends mapped to different chromosomes or orphan reads).
+ OPTIONS:
- rmdupse samtools rmdupse <input.srt.bam> <out.bam>
+ -s Remove duplicate for single-end reads. By default,
+ the command works for paired-end reads only.
- Remove potential duplicates for single-ended reads. This com-
- mand will treat all reads as single-ended even if they are
- paired in fact.
+ -S Treat paired-end reads and single-end reads.
-
fillmd samtools fillmd [-e] <aln.bam> <ref.fasta>
+
calmd samtools calmd [-eubS] <aln.bam> <ref.fasta>
Generate the MD tag. If the MD tag is already present, this
command will give a warning if the MD tag generated is dif-
- ferent from the existing tag.
+ ferent from the existing tag. Output SAM by default.
OPTIONS:
the aligned reference base. Indel caller does not
support the = bases at the moment.
+ -u Output uncompressed BAM
+
+ -b Output compressed BAM
+
+ -S The input is SAM with header lines
SAM FORMAT
Each bit in the FLAG field is defined as:
- +-------+--------------------------------------------------+
- | 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 |
- +-------+--------------------------------------------------+
+ +-------+-----+--------------------------------------------------+
+ | Flag | Chr | Description |
+ +-------+-----+--------------------------------------------------+
+ |0x0001 | p | the read is paired in sequencing |
+ |0x0002 | P | the read is mapped in a proper pair |
+ |0x0004 | u | the query sequence itself is unmapped |
+ |0x0008 | U | the mate is unmapped |
+ |0x0010 | r | strand of the query (1 for reverse) |
+ |0x0020 | R | strand of the mate |
+ |0x0040 | 1 | the read is the first read in a pair |
+ |0x0080 | 2 | the read is the second read in a pair |
+ |0x0100 | s | the alignment is not primary |
+ |0x0200 | f | the read fails platform/vendor quality checks |
+ |0x0400 | d | the read is either a PCR or an optical duplicate |
+ +-------+-----+--------------------------------------------------+
LIMITATIONS
o Unaligned words used in bam_import.c, bam_endian.h, bam.c and
bam_aux.c.
- o CIGAR operation P is not properly handled at the moment.
-
o In merging, the input files are required to have the same number of
reference sequences. The requirement can be relaxed. In addition,
merging does not reconstruct the header dictionaries automatically.
Endusers have to provide the correct header. Picard is better at
merging.
- o Samtools' rmdup does not work for single-end data and does not remove
- duplicates across chromosomes. Picard is better.
+ o Samtools paired-end rmdup does not work for unpaired reads (e.g.
+ orphan reads or ends mapped to different chromosomes). If this is a
+ concern, please use Picard's MarkDuplicate which correctly handles
+ these cases, although a little slower.
AUTHOR
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 speci-
+ people in the 1000 Genomes Project contributed to the SAM format speci-
fication.
-samtools-0.1.7 10 November 2009 samtools(1)
+samtools-0.1.8 11 July 2010 samtools(1)
projects / samtools.git / blobdiff