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;
-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.
- -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.
+ -l STR Only output reads in library STR [null]
-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]
+ -q INT Skip alignments with MAPQ smaller than INT [0]
- -F INT Skip alignments with bits present in INT [0]
+ -r STR Only output reads in read group STR [null]
- -q INT Skip alignments with MAPQ smaller than INT [0]
+ -R FILE Output reads in read groups listed in FILE [null]
- -l STR Only output reads in library STR [null]
+ -S Input is in SAM. If @SQ header lines are absent, the
+ `-t' option is required.
- -r STR Only output reads in read group STR [null]
+ -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.
+ -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 [...]]
- 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
- 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
+ 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
- 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 `$' marks the end of a read seg-
- ment.
-
- If option -c is applied, the consensus base, Phred-scaled
- consensus quality, SNP quality (i.e. the Phred-scaled proba-
+ end of a read are all encoded at the read base column. At
+ this column, a dot stands for a match to the reference base
+ on the forward strand, a comma for a match on the reverse
+ strand, a '>' or '<' for a reference skip, `ACGTN' for a mis-
+ match on the forward strand and `acgtn' for a mismatch on the
+ reverse strand. A pattern `\+[0-9]+[ACGTNacgtn]+' indicates
+ there is an insertion between this reference position and the
+ next reference position. The length of the insertion is given
+ by the integer in the pattern, followed by the inserted
+ sequence. Similarly, a pattern `-[0-9]+[ACGTNacgtn]+' repre-
+ sents a deletion from the reference. The deleted bases will
+ be presented as `*' in the following lines. Also at the read
+ base column, a symbol `^' marks the start of a read. The
+ ASCII of the character following `^' minus 33 gives the map-
+ ping quality. A symbol `$' 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,
+ 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.
+ 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]
+
+ -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>
- tview samtools tview <in.sorted.bam> [ref.fasta]
+ 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.
- 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'.
+
+ 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
+
+
+ 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.
+ 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 [-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.
+ 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
+
+ -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
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
+ 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
+ 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
+ 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-
+ Ruan from Beijing Genomics Institute wrote the RAZF library. Various
+ people in the 1000 Genomes Project contributed to the SAM format speci-
fication.
-samtools-0.1.7 10 November 2009 samtools(1)
+samtools-0.1.9 27 October 2010 samtools(1)
projects / samtools.git / blobdiff