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 faidx ref.fasta
- samtools pileup -f ref.fasta aln.sorted.bam
+ samtools pileup -vcf ref.fasta aln.sorted.bam
+
+ samtools mpileup -C50 -agf ref.fasta -r chr3:1,000-2,000 in1.bam
+ in2.bam
samtools tview aln.sorted.bam ref.fasta
DESCRIPTION
- Samtools is a set of utilities that manipulate alignments in the BAM
+ 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
+ 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
+ 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 or
- HTTP server if the BAM file name starts with `ftp://' or `http://'.
- Samtools checks the current working directory for the index file and
- will download the index upon absence. Samtools does not retrieve the
+ Samtools is also able to open a BAM (not SAM) file on a remote FTP or
+ HTTP server if the BAM file name starts with `ftp://' or `http://'.
+ Samtools checks the current working directory for the index file and
+ will download the index upon absence. Samtools does not retrieve the
entire alignment file unless it is asked to do so.
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 [...]]
+ 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
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'. The coordinate is 1-based.
+ 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
- when the output is piped to another samtools command.
+ -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]
+
+ -F INT Skip alignments with bits present in INT [0]
-h Include the header in the output.
-H Output the header only.
+ -l STR Only output reads in library STR [null]
+
+ -o FILE Output file [stdout]
+
+ -q INT Skip alignments with MAPQ smaller than INT [0]
+
+ -r STR Only output reads in read group STR [null]
+
+ -R FILE Output reads in read groups listed in FILE [null]
+
-S Input is in SAM. If @SQ header lines are absent, the
`-t' option is required.
`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
- in the FLAG field. INT can be in hex in the format of
- /^0x[0-9A-F]+/ [0]
-
- -F INT Skip alignments with bits present in INT [0]
-
- -q INT Skip alignments with MAPQ smaller than INT [0]
-
- -l STR Only output reads in library STR [null]
-
- -r STR Only output reads in read group STR [null]
+ -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.
- faidx samtools faidx <ref.fasta> [region1 [...]]
+ tview samtools tview <in.sorted.bam> [ref.fasta]
- 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.
+ 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
- pairDiffRate] <in.bam>|<in.sam>
+ pileup samtools pileup [-2sSBicv] [-f in.ref.fasta] [-t in.ref_list]
+ [-l in.site_list] [-C capMapQ] [-M maxMapQ] [-T theta] [-N
+ nHap] [-r pairDiffRate] [-m mask] [-d maxIndelDepth] [-G
+ indelPrior] <in.bam>|<in.sam>
Print the alignment in the pileup format. In the pileup for-
mat, each line represents a genomic position, consisting of
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 `$' marks the end of a read seg-
- ment.
-
- If option -c is applied, the consensus base, consensus qual-
- ity, SNP quality and RMS mapping quality of the reads cover-
- ing the site will be inserted between the `reference base'
- and the `read bases' columns. An indel occupies an additional
+ strand, a '>' or '<' for a reference skip, `ACGTN' for a mis-
+ match on the forward strand and `acgtn' for a mismatch on the
+ reverse strand. A pattern `\+[0-9]+[ACGTNacgtn]+' indicates
+ there is an insertion between this reference position and the
+ next reference position. The length of the insertion is given
+ by the integer in the pattern, followed by the inserted
+ sequence. Similarly, a pattern `-[0-9]+[ACGTNacgtn]+' repre-
+ sents a deletion from the reference. The deleted bases will
+ be presented as `*' in the following lines. Also at the read
+ base column, a symbol `^' marks the start of a read. The
+ ASCII of the character following `^' minus 33 gives the map-
+ ping quality. A symbol `$' marks the end of a read segment.
+
+ 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,
RMS mapping quality, # covering reads, the first alllele, the
supporting the second allele and # reads containing indels
different from the top two alleles.
+ The position of indels is offset by -1.
+
OPTIONS:
+ -B Disable the BAQ computation. See the mpileup com-
+ mand for details.
- -s Print the mapping quality as the last column. This
- option makes the output easier to parse, although
- this format is not space efficient.
+ -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.
+ -C INT Coefficient for downgrading the mapping quality of
+ poorly mapped reads. See the mpileup command for
+ details. [0]
- -S The input file is in SAM.
+ -d INT Use the first NUM reads in the pileup for indel
+ calling for speed up. Zero for unlimited. [1024]
+ -f FILE The reference sequence in the FASTA format. Index
+ file FILE.fai will be created if absent.
+
+ -g Generate genotype likelihood in the binary GLFv3
+ format. This option suppresses -c, -i and -s. This
+ option is deprecated by the mpileup command.
-i Only output pileup lines containing indels.
+ -I INT Phred probability of an indel in sequencing/prep.
+ [40]
- -f FILE The reference sequence in the FASTA format. Index
- file FILE.fai will be created if absent.
+ -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
+ -m INT Filter reads with flag containing bits in INT
+ [1796]
-M INT Cap mapping quality at INT [60]
+ -N INT Number of haplotypes in the sample (>=2) [2]
+
+ -r FLOAT Expected fraction of differences between a pair of
+ haplotypes [0.001]
- -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
+ -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.
+
+ -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.
+ assumes in BAM format. -s together with -l as in
+ the default format we may not know the mapping
+ quality.
+ -T FLOAT The theta parameter (error dependency coefficient)
+ in the maq consensus calling model [0.85]
- -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.
+ mpileup samtools mpileup [-Bug] [-C capQcoef] [-r reg] [-f in.fa] [-l
+ list] [-M capMapQ] [-Q minBaseQ] [-q minMapQ] in.bam [in2.bam
+ [...]]
- -c Call the consensus sequence using MAQ consensus
- model. Options -T, -N, -I and -r are only effective
- when -c or -g is in use.
+ Generate BCF or pileup for one or multiple BAM files. Align-
+ ment records are grouped by sample identifiers in @RG header
+ lines. If sample identifiers are absent, each input file is
+ regarded as one sample.
+ OPTIONS:
- -g Generate genotype likelihood in the binary GLFv3
- format. This option suppresses -c, -i and -s.
+ -B Disable probabilistic realignment for the computation
+ of base alignment quality (BAQ). BAQ is the Phred-
+ scaled probability of a read base being misaligned.
+ Applying this option greatly helps to reduce false
+ SNPs caused by misalignments.
+ -C INT Coefficient for downgrading mapping quality for reads
+ containing excessive mismatches. Given a read with a
+ phred-scaled probability q of being generated from
+ the mapped position, the new mapping quality is about
+ sqrt((INT-q)/INT)*INT. A zero value disables this
+ functionality; if enabled, the recommended value is
+ 50. [0]
- -T FLOAT The theta parameter (error dependency coefficient)
- in the maq consensus calling model [0.85]
+ -f FILE The reference file [null]
+ -g Compute genotype likelihoods and output them in the
+ binary call format (BCF).
- -N INT Number of haplotypes in the sample (>=2) [2]
+ -u Similar to -g except that the output is uncompressed
+ BCF, which is preferred for pipeing.
+ -l FILE File containing a list of sites where pileup or BCF
+ is outputted [null]
- -r FLOAT Expected fraction of differences between a pair of
- haplotypes [0.001]
+ -q INT Minimum mapping quality for an alignment to be used
+ [0]
+ -Q INT Minimum base quality for a base to be considered [13]
- -I INT Phred probability of an indel in sequencing/prep.
- [40]
+ -r STR Only generate pileup in region STR [all sites]
+ 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 [-nur] [-h inh.sam] [-R reg] <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 STR Merge files in the specified region indicated by STR
+
+ -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
+
+ -u Uncompressed BAM output
- 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'.
+ 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>
+ 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.
+ 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:
+ -s Remove duplicate for single-end reads. By default,
+ the command works for paired-end reads only.
- rmdupse samtools rmdupse <input.srt.bam> <out.bam>
-
- 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 [-eubSr] [-C capQcoef] <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.
+ 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. Output SAM by default.
OPTIONS:
- -e Convert a the read base to = if it is identical to
- the aligned reference base. Indel caller does not
+ -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.
+ -u Output uncompressed BAM
+
+ -b Output compressed BAM
+
+ -S The input is SAM with header lines
+
+ -C INT Coefficient to cap mapping quality of poorly mapped
+ reads. See the pileup command for details. [0]
+
+ -r Perform probabilistic realignment to compute BAQ,
+ which will be used to cap base quality.
SAM FORMAT
- SAM is TAB-delimited. Apart from the header lines, which are started
+ SAM is TAB-delimited. Apart from the header lines, which are started
with the `@' symbol, each alignment line consists of:
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 |
+ +-------+-----+--------------------------------------------------+
+
+EXAMPLES
+ o Import SAM to BAM when @SQ lines are present in the header:
+
+ samtools view -bS aln.sam > aln.bam
+
+ If @SQ lines are absent:
+
+ samtools faidx ref.fa
+ samtools view -bt ref.fa.fai aln.sam > aln.bam
+
+ where ref.fa.fai is generated automatically by the faidx command.
+
+
+ o Attach the RG tag while merging sorted alignments:
+
+ perl -e 'print "@RG\tID:ga\tSM:hs\tLB:ga\tPL:Illu-
+ mina\n@RG\tID:454\tSM:hs\tLB:454\tPL:454\n"' > rg.txt
+ samtools merge -rh rg.txt merged.bam ga.bam 454.bam
+
+ The value in a RG tag is determined by the file name the read is com-
+ ing from. In this example, in the merged.bam, reads from ga.bam will
+ be attached RG:Z:ga, while reads from 454.bam will be attached
+ RG:Z:454.
+
+
+ o Call SNPs and short indels for one diploid individual:
+
+ samtools pileup -vcf ref.fa aln.bam > var.raw.plp
+ samtools.pl varFilter -D 100 var.raw.plp > var.flt.plp
+ awk '($3=="*"&&$6>=50)||($3!="*"&&$6>=20)' var.flt.plp >
+ var.final.plp
+
+ The -D option of varFilter controls the maximum read depth, which
+ should be adjusted to about twice the average read depth. One may
+ consider to add -C50 to pileup if mapping quality is overestimated
+ for reads containing excessive mismatches. Applying this option usu-
+ ally helps BWA-short but may not other mappers. It also potentially
+ increases reference biases.
+
+
+ o Call SNPs (not short indels) for multiple diploid individuals:
+
+ samtools mpileup -augf ref.fa *.bam | bcftools view -bcv - >
+ snp.raw.bcf
+ bcftools view snp.raw.bcf | vcfutils.pl filter4vcf -D 2000 | bgzip
+ > snp.flt.vcf.gz
+
+ Individuals are identified from the SM tags in the @RG header lines.
+ Individuals can be pooled in one alignment file; one individual can
+ also be separated into multiple files. Similarly, one may consider to
+ apply -C50 to mpileup. SNP calling in this way also works for single
+ sample and has the advantage of enabling more powerful filtering. The
+ drawback is the lack of short indel calling, which may be implemented
+ in future.
+
+
+ o Derive the allele frequency spectrum (AFS) on a list of sites from
+ multiple individuals:
+
+ samtools mpileup -gf ref.fa *.bam > all.bcf
+ bcftools view -bl sites.list all.bcf > sites.bcf
+ bcftools view -cGP cond2 sites.bcf > /dev/null 2> sites.1.afs
+ bcftools view -cGP sites.1.afs sites.bcf > /dev/null 2> sites.2.afs
+ bcftools view -cGP sites.2.afs sites.bcf > /dev/null 2> sites.3.afs
+ ......
+
+ where sites.list contains the list of sites with each line consisting
+ of the reference sequence name and position. The following bcftools
+ commands estimate AFS by EM.
+
+
+ o Dump BAQ applied alignment for other SNP callers:
+
+ samtools calmd -br aln.bam > aln.baq.bam
+
+ It adds and corrects the NM and MD tags at the same time. The calmd
+ command also comes with the -C option, the same as the on in pileup
+ and mpileup. Apply if it helps.
+
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-0.1.6 2 September 2009 samtools(1)
+samtools-0.1.9 27 October 2010 samtools(1)
projects / samtools.git / blobdiff