-.TH samtools 1 "6 July 2009" "samtools-0.1.5" "Bioinformatics tools"
+.TH samtools 1 "27 October 2010" "samtools-0.1.9" "Bioinformatics tools"
.SH NAME
.PP
samtools - Utilities for the Sequence Alignment/Map (SAM) format
.PP
samtools index aln.sorted.bam
.PP
+samtools idxstats aln.sorted.bam
+.PP
samtools view aln.sorted.bam chr2:20,100,000-20,200,000
.PP
samtools merge out.bam in1.bam in2.bam in3.bam
.PP
samtools faidx ref.fasta
.PP
-samtools pileup -f ref.fasta aln.sorted.bam
+samtools pileup -vcf ref.fasta aln.sorted.bam
+.PP
+samtools mpileup -C50 -agf ref.fasta -r chr3:1,000-2,000 in1.bam in2.bam
.PP
samtools tview aln.sorted.bam ref.fasta
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
-server if the BAM file name starts with `ftp://'. Samtools checks the
-current working directory for the index file and will download the index
-upon absence. Samtools achieves random FTP file access with the `REST'
-ftp command. It does not retrieve the entire alignment file unless it is
-asked to do so.
+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.
.SH COMMANDS AND OPTIONS
.TP 10
-.B 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>
-
-.TP
-.B sort
-samtools sort [-n] [-m maxMem] <in.bam> <out.prefix>
-
-Sort alignments by leftmost coordinates. File
-.I <out.prefix>.bam
-will be created. This command may also create temporary files
-.I <out.prefix>.%d.bam
-when the whole alignment cannot be fitted into memory (controlled by
-option -m).
-
-.B OPTIONS:
-.RS
-.TP 8
-.B -n
-Sort by read names rather than by chromosomal coordinates
-.TP
-.B -m INT
-Approximately the maximum required memory. [500000000]
-.RE
-
-.TP
-.B merge
-samtools merge [-n] <out.bam> <in1.bam> <in2.bam> [...]
-
-Merge multiple sorted alignments. The header of
-.I <in1.bam>
-will be copied to
-.I <out.bam>
-and the headers of other files will be ignored.
-
-.B OPTIONS:
-.RS
-.TP 8
-.B -n
-The input alignments are sorted by read names rather than by chromosomal
-coordinates
-.RE
-
-.TP
-.B index
-samtools index <aln.bam>
-
-Index sorted alignment for fast random access. Index file
-.I <aln.bam>.bai
-will be created.
-
-.TP
.B view
samtools view [-bhuHS] [-t in.refList] [-o output] [-f reqFlag] [-F
-skipFlag] [-q minMapQ] [-l library] [-r readGroup] <in.bam>|<in.sam> [region1 [...]]
+skipFlag] [-q minMapQ] [-l library] [-r readGroup] [-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.
+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.
.B OPTIONS:
.RS
.B -b
Output in the BAM format.
.TP
-.B -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.
+.BI -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]
+.TP
+.BI -F " INT"
+Skip alignments with bits present in INT [0]
.TP
.B -h
Include the header in the output.
.B -H
Output the header only.
.TP
+.BI -l " STR"
+Only output reads in library STR [null]
+.TP
+.BI -o " FILE"
+Output file [stdout]
+.TP
+.BI -q " INT"
+Skip alignments with MAPQ smaller than INT [0]
+.TP
+.BI -r " STR"
+Only output reads in read group STR [null]
+.TP
+.BI -R " FILE"
+Output reads in read groups listed in
+.I FILE
+[null]
+.TP
.B -S
Input is in SAM. If @SQ header lines are absent, the
.B `-t'
option is required.
.TP
-.B -t FILE
+.BI -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
.I <in.ref_list>
file.
.TP
-.B -o FILE
-Output file [stdout]
-.TP
-.B -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]
-.TP
-.B -F INT
-Skip alignments with bits present in INT [0]
-.TP
-.B -q INT
-Skip alignments with MAPQ smaller than INT [0]
-.TP
-.B -l STR
-Only output reads in library STR [null]
-.TP
-.B -r STR
-Only output reads in read group STR [null]
+.B -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.
.RE
.TP
-.B faidx
-samtools faidx <ref.fasta> [region1 [...]]
+.B tview
+samtools tview <in.sorted.bam> [ref.fasta]
-Index reference sequence in the FASTA format or extract subsequence from
-indexed reference sequence. If no region is specified,
-.B faidx
-will index the file and create
-.I <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
-.B RAZF
-format.
+Text alignment viewer (based on the ncurses library). In the viewer,
+press `?' for help and press `g' to check the alignment start from a
+region in the format like `chr10:10,000,000' or `=10,000,000' when
+viewing the same reference sequence.
.TP
.B 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>
+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 format, each
line represents a genomic position, consisting of chromosome name,
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 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]+' 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 subsequence on the read separated by `N/S/H' CIGAR
-operations. The ASCII of the character following `^' minus 33 gives the
-mapping quality. A symbol `$' marks the end of a read segment.
+a '>' or '<' for a reference skip, `ACGTN' for a mismatch on the forward
+strand and `acgtn' for a mismatch on the reverse strand. A pattern
+`\\+[0-9]+[ACGTNacgtn]+' indicates there is an insertion between this
+reference position and the next reference position. The length of the
+insertion is given by the integer in the pattern, followed by the
+inserted sequence. Similarly, a pattern `-[0-9]+[ACGTNacgtn]+'
+represents a deletion from the reference. The deleted bases will be
+presented as `*' in the following lines. Also at the read base column, a
+symbol `^' marks the start of a read. The ASCII of the character
+following `^' minus 33 gives the mapping quality. A symbol `$' marks the
+end of a read segment.
If option
.B -c
-is applied, the consensus base, consensus quality, SNP quality and 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,
-coordinate, 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 different from the top two alleles.
+is applied, the consensus base, Phred-scaled consensus quality, SNP
+quality (i.e. the Phred-scaled probability 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, coordinate, 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 different from the top two alleles.
+
+The position of indels is offset by -1.
.B OPTIONS:
.RS
-
.TP 10
-.B -s
-Print the mapping quality as the last column. This option makes the
-output easier to parse, although this format is not space efficient.
-
+.B -B
+Disable the BAQ computation. See the
+.B mpileup
+command for details.
.TP
-.B -S
-The input file is in SAM.
-
+.B -c
+Call the consensus sequence using SOAPsnp consensus model. Options
+.BR -T ", " -N ", " -I " and " -r
+are only effective when
+.BR -c " or " -g
+is in use.
.TP
-.B -i
-Only output pileup lines containing indels.
-
+.BI -C " INT"
+Coefficient for downgrading the mapping quality of poorly mapped
+reads. See the
+.B mpileup
+command for details. [0]
+.TP
+.BI -d " INT"
+Use the first
+.I NUM
+reads in the pileup for indel calling for speed up. Zero for unlimited. [1024]
.TP
-.B -f FILE
+.BI -f " FILE"
The reference sequence in the FASTA format. Index file
.I FILE.fai
will be created if
absent.
-
.TP
-.B -M INT
+.B -g
+Generate genotype likelihood in the binary GLFv3 format. This option
+suppresses -c, -i and -s. This option is deprecated by the
+.B mpileup
+command.
+.TP
+.B -i
+Only output pileup lines containing indels.
+.TP
+.BI -I " INT"
+Phred probability of an indel in sequencing/prep. [40]
+.TP
+.BI -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
+.TP
+.BI -m " INT"
+Filter reads with flag containing bits in
+.I INT
+[1796]
+.TP
+.BI -M " INT"
Cap mapping quality at INT [60]
-
.TP
-.B -t FILE
+.BI -N " INT"
+Number of haplotypes in the sample (>=2) [2]
+.TP
+.BI -r " FLOAT"
+Expected fraction of differences between a pair of haplotypes [0.001]
+.TP
+.B -s
+Print the mapping quality as the last column. This option makes the
+output easier to parse, although this format is not space efficient.
+.TP
+.B -S
+The input file is in SAM.
+.TP
+.BI -t " FILE"
List of reference names ane sequence lengths, in the format described
for the
.B import
command. If this option is present, samtools assumes the input
.I <in.alignment>
is in SAM format; otherwise it assumes in BAM format.
-
-.TP
-.B -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
.B -s
together with
.B -l
as in the default format we may not know the mapping quality.
+.TP
+.BI -T " FLOAT"
+The theta parameter (error dependency coefficient) in the maq consensus
+calling model [0.85]
+.RE
.TP
-.B -c
-Call the consensus sequence using MAQ consensus model. Options
-.B -T,
-.B -N,
-.B -I
-and
-.B -r
-are only effective when
-.B -c
-or
-.B -g
-is in use.
+.B mpileup
+samtools mpileup [-Bug] [-C capQcoef] [-r reg] [-f in.fa] [-l list] [-M capMapQ] [-Q minBaseQ] [-q minMapQ] in.bam [in2.bam [...]]
+Generate BCF or pileup for one or multiple BAM files. Alignment records
+are grouped by sample identifiers in @RG header lines. If sample
+identifiers are absent, each input file is regarded as one sample.
+
+.B OPTIONS:
+.RS
+.TP 8
+.B -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.
+.TP
+.BI -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]
+.TP
+.BI -f " FILE"
+The reference file [null]
.TP
.B -g
-Generate genotype likelihood in the binary GLFv3 format. This option
-suppresses -c, -i and -s.
+Compute genotype likelihoods and output them in the binary call format (BCF).
+.TP
+.B -u
+Similar to
+.B -g
+except that the output is uncompressed BCF, which is preferred for pipeing.
+.TP
+.BI -l " FILE"
+File containing a list of sites where pileup or BCF is outputted [null]
+.TP
+.BI -q " INT"
+Minimum mapping quality for an alignment to be used [0]
+.TP
+.BI -Q " INT"
+Minimum base quality for a base to be considered [13]
+.TP
+.BI -r " STR"
+Only generate pileup in region
+.I STR
+[all sites]
+.RE
.TP
-.B -T FLOAT
-The theta parameter (error dependency coefficient) in the maq consensus
-calling model [0.85]
+.B reheader
+samtools reheader <in.header.sam> <in.bam>
+
+Replace the header in
+.I in.bam
+with the header in
+.I in.header.sam.
+This command is much faster than replacing the header with a
+BAM->SAM->BAM conversion.
.TP
-.B -N INT
-Number of haplotypes in the sample (>=2) [2]
+.B sort
+samtools sort [-no] [-m maxMem] <in.bam> <out.prefix>
+
+Sort alignments by leftmost coordinates. File
+.I <out.prefix>.bam
+will be created. This command may also create temporary files
+.I <out.prefix>.%d.bam
+when the whole alignment cannot be fitted into memory (controlled by
+option -m).
+.B OPTIONS:
+.RS
+.TP 8
+.B -o
+Output the final alignment to the standard output.
.TP
-.B -r FLOAT
-Expected fraction of differences between a pair of haplotypes [0.001]
+.B -n
+Sort by read names rather than by chromosomal coordinates
+.TP
+.B -m INT
+Approximately the maximum required memory. [500000000]
+.RE
.TP
-.B -I INT
-Phred probability of an indel in sequencing/prep. [40]
+.B 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
+.IR inh.sam ,
+if any, must all refer to the same set of reference sequences.
+The header reference list and (unless overridden by
+.BR -h )
+`@' headers of
+.I in1.bam
+will be copied to
+.IR out.bam ,
+and the headers of other files will be ignored.
+.B OPTIONS:
+.RS
+.TP 8
+.BI -h " FILE"
+Use the lines of
+.I FILE
+as `@' headers to be copied to
+.IR out.bam ,
+replacing any header lines that would otherwise be copied from
+.IR in1.bam .
+.RI ( FILE
+is actually in SAM format, though any alignment records it may contain
+are ignored.)
+.TP
+.BI -R " STR"
+Merge files in the specified region indicated by
+.I STR
+.TP
+.B -r
+Attach an RG tag to each alignment. The tag value is inferred from file names.
+.TP
+.B -n
+The input alignments are sorted by read names rather than by chromosomal
+coordinates
+.TP
+.B -u
+Uncompressed BAM output
.RE
.TP
-.B tview
-samtools tview <in.sorted.bam> [ref.fasta]
+.B index
+samtools index <aln.bam>
-Text alignment viewer (based on the ncurses library). In the viewer,
-press `?' for help and press `g' to check the alignment start from a
-region in the format like `chr10:10,000,000'. Note that if the region
-showed on the screen contains no mapped reads, a blank screen will be
-seen. This is a known issue and will be improved later.
+Index sorted alignment for fast random access. Index file
+.I <aln.bam>.bai
+will be created.
-.RE
+.TP
+.B 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.
+
+.TP
+.B faidx
+samtools faidx <ref.fasta> [region1 [...]]
+
+Index reference sequence in the FASTA format or extract subsequence from
+indexed reference sequence. If no region is specified,
+.B faidx
+will index the file and create
+.I <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
+.B RAZF
+format.
.TP
.B fixmate
.TP
.B rmdup
-samtools rmdup <input.srt.bam> <out.bam>
+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
+In the paired-end mode, this command
.B ONLY
-works with FR orientation and requires ISIZE is correctly set.
-
-.RE
-
-.TP
-.B rmdupse
-samtools rmdupse <input.srt.bam> <out.bam>
-
-Remove potential duplicates for single-ended reads. This command will
-treat all reads as single-ended even if they are paired in fact.
+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).
+.B OPTIONS:
+.RS
+.TP 8
+.B -s
+Remove duplicate for single-end reads. By default, the command works for
+paired-end reads only.
+.TP 8
+.B -S
+Treat paired-end reads and single-end reads.
.RE
.TP
-.B fillmd
-samtools
fillmd [-e] <aln.bam> <ref.fasta>
+.B 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 different from the existing
-tag.
+tag. Output SAM by default.
.B OPTIONS:
.RS
.B -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.
-
+.TP
+.B -u
+Output uncompressed BAM
+.TP
+.B -b
+Output compressed BAM
+.TP
+.B -S
+The input is SAM with header lines
+.TP
+.BI -C " INT"
+Coefficient to cap mapping quality of poorly mapped reads. See the
+.B pileup
+command for details. [0]
+.TP
+.B -r
+Perform probabilistic realignment to compute BAQ, which will be used to
+cap base quality.
.RE
.SH SAM FORMAT
.TS
center box;
-cb | cb
-l | l .
-Flag Description
+cb | cb | cb
+l | c | l .
+Flag Chr 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
+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
.TE
+.SH EXAMPLES
+.IP o 2
+Import SAM to BAM when
+.B @SQ
+lines are present in the header:
+
+ samtools view -bS aln.sam > aln.bam
+
+If
+.B @SQ
+lines are absent:
+
+ samtools faidx ref.fa
+ samtools view -bt ref.fa.fai aln.sam > aln.bam
+
+where
+.I ref.fa.fai
+is generated automatically by the
+.B faidx
+command.
+
+.IP o 2
+Attach the
+.B RG
+tag while merging sorted alignments:
+
+ perl -e 'print "@RG\\tID:ga\\tSM:hs\\tLB:ga\\tPL:Illumina\\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
+.B RG
+tag is determined by the file name the read is coming from. In this
+example, in the
+.IR merged.bam ,
+reads from
+.I ga.bam
+will be attached
+.IR RG:Z:ga ,
+while reads from
+.I 454.bam
+will be attached
+.IR RG:Z:454 .
+
+.IP o 2
+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
+.B -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
+.B -C50
+to
+.B pileup
+if mapping quality is overestimated for reads containing excessive
+mismatches. Applying this option usually helps
+.B BWA-short
+but may not other mappers. It also potentially increases reference
+biases.
+
+.IP o 2
+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
+.B SM
+tags in the
+.B @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
+.B -C50
+to
+.BR 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.
+
+.IP o 2
+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
+.I sites.list
+contains the list of sites with each line consisting of the reference
+sequence name and position. The following
+.B bcftools
+commands estimate AFS by EM.
+
+.IP o 2
+Dump BAQ applied alignment for other SNP callers:
+
+ samtools calmd -br aln.bam > aln.baq.bam
+
+It adds and corrects the
+.B NM
+and
+.B MD
+tags at the same time. The
+.B calmd
+command also comes with the
+.B -C
+option, the same as the on in
+.B pileup
+and
+.BR mpileup .
+Apply if it helps.
+
.SH LIMITATIONS
.PP
.IP o 2
Unaligned words used in bam_import.c, bam_endian.h, bam.c and bam_aux.c.
.IP o 2
-CIGAR operation P is not properly handled at the moment.
+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.
+.IP o 2
+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.
.SH AUTHOR
.PP
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
+people in the 1000 Genomes Project contributed to the SAM format
specification.
.SH SEE ALSO
.PP
-Samtools website: http://samtools.sourceforge.net
+Samtools website: <http://samtools.sourceforge.net>
projects / samtools.git / blobdiff