-.TH samtools 1 "2 September 2009" "samtools-0.1.6" "Bioinformatics tools"
+.TH samtools 1 "16 March 2011" "samtools-0.1.14" "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 -gf ref.fasta -r chr3:1,000-2,000 in1.bam in2.bam
.PP
samtools tview aln.sorted.bam ref.fasta
.SH COMMANDS AND OPTIONS
.TP 10
-.B import
-samtools import <in.ref_list> <in.sam> <out.bam>
+.B view
+samtools view [-bchuHS] [-t in.refList] [-o output] [-f reqFlag] [-F
+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' (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
+.TP 8
+.B -b
+Output in the BAM format.
+.TP
+.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.
+.TP
+.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 -c
+Instead of printing the alignments, only count them and print the
+total number. All filter options, such as
+.B `-f',
+.B `-F'
+and
+.B `-q'
+, are taken into account.
+.TP
+.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
+reference sequences in sorting. If you run `samtools faidx <ref.fa>',
+the resultant index file
+.I <ref.fa>.fai
+can be used as this
+.I <in.ref_list>
+file.
+.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.
+.RE
+
+.TP
+.B 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 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 mpileup
+samtools mpileup [-EBug] [-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 10
+.B -A
+Do not skip anomalous read pairs in variant calling.
+.TP
+.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 for BWA is 50. [0]
+.TP
+.BI -d \ INT
+At a position, read maximally
+.I INT
+reads per input BAM. [250]
+.TP
+.B -D
+Output per-sample read depth
+.TP
+.BI -e \ INT
+Phred-scaled gap extension sequencing error probability. Reducing
+.I INT
+leads to longer indels. [20]
+.TP
+.B -E
+Extended BAQ computation. This option helps sensitivity especially for MNPs, but may hurt
+specificity a little bit.
+.TP
+.BI -f \ FILE
+The reference file [null]
+.TP
+.B -g
+Compute genotype likelihoods and output them in the binary call format (BCF).
+.TP
+.BI -h \ INT
+Coefficient for modeling homopolymer errors. Given an
+.IR l -long
+homopolymer
+run, the sequencing error of an indel of size
+.I s
+is modeled as
+.IR INT * s / l .
+[100]
+.TP
+.B -I
+Do not perform INDEL calling
+.TP
+.BI -l \ FILE
+File containing a list of sites where pileup or BCF is outputted [null]
+.TP
+.BI -L \ INT
+Skip INDEL calling if the average per-sample depth is above
+.IR INT .
+[250]
+.TP
+.BI -o \ INT
+Phred-scaled gap open sequencing error probability. Reducing
+.I INT
+leads to more indel calls. [40]
+.TP
+.BI -P \ STR
+Comma dilimited list of platforms (determined by
+.BR @RG-PL )
+from which indel candidates are obtained. It is recommended to collect
+indel candidates from sequencing technologies that have low indel error
+rate such as ILLUMINA. [all]
+.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]
+.TP
+.B -S
+Output per-sample Phred-scaled strand bias P-value
+.TP
+.B -u
+Similar to
+.B -g
+except that the output is uncompressed BCF, which is preferred for piping.
+.RE
+
+.TP
+.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.
-Since 0.1.4, this command is an alias of:
+.TP
+.B cat
+samtools cat [-h header.sam] [-o out.bam] <in1.bam> <in2.bam> [ ... ]
-samtools view -bt <in.ref_list> -o <out.bam> <in.sam>
+Concatenate BAMs. The sequence dictionary of each input BAM must be identical,
+although this command does not check this. This command uses a similar trick
+to
+.B reheader
+which enables fast BAM concatenation.
.TP
.B sort
-samtools sort [-n] [-m maxMem] <in.bam> <out.prefix>
+samtools sort [-no] [-m maxMem] <in.bam> <out.prefix>
Sort alignments by leftmost coordinates. File
.I <out.prefix>.bam
.B OPTIONS:
.RS
.TP 8
+.B -o
+Output the final alignment to the standard output.
+.TP
.B -n
Sort by read names rather than by chromosomal coordinates
.TP
-.B -m INT
+.BI -m \ INT
Approximately the maximum required memory. [500000000]
.RE
.TP
.B merge
-samtools merge [-h inh.sam] [-n] <out.bam> <in1.bam> <in2.bam> [...]
+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
.B OPTIONS:
.RS
.TP 8
-.B -h FILE
+.BI -h \ FILE
Use the lines of
.I FILE
as `@' headers to be copied to
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
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 [...]]
+.B idxstats
+samtools idxstats <aln.bam>
-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.
+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
+samtools fixmate <in.nameSrt.bam> <out.bam>
+
+Fill in mate coordinates, ISIZE and mate related flags from a
+name-sorted alignment.
+
+.TP
+.B 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.
+In the paired-end mode, this command
+.B 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).
.B OPTIONS:
.RS
.TP 8
-.B -b
-Output in the BAM format.
+.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 -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.
+.B calmd
+samtools calmd [-EeubSr] [-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. Output SAM by default.
+
+.B OPTIONS:
+.RS
+.TP 8
+.B -A
+When used jointly with
+.B -r
+this option overwrites the original base quality.
+.TP 8
+.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 -h
-Include the header in the output.
+.B -u
+Output uncompressed BAM
.TP
-.B -H
-Output the header only.
+.B -b
+Output compressed BAM
.TP
.B -S
-Input is in SAM. If @SQ header lines are absent, the
-.B `-t'
-option is required.
-.TP
-.B -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
-.I <ref.fa>.fai
-can be used as this
-.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]
+The input is SAM with header lines
.TP
-.B -F INT
-Skip alignments with bits present in INT [0]
+.BI -C \ INT
+Coefficient to cap mapping quality of poorly mapped reads. See the
+.B pileup
+command for details. [0]
.TP
-.B -q INT
-Skip alignments with MAPQ smaller than INT [0]
+.B -r
+Compute the BQ tag (without -A) or cap base quality by BAQ (with -A).
.TP
-.B -l STR
-Only output reads in library STR [null]
+.B -E
+Extended BAQ calculation. This option trades specificity for sensitivity, though the
+effect is minor.
+.RE
+
.TP
-.B -r STR
-Only output reads in read group STR [null]
+.B targetcut
+samtools targetcut [-Q minBaseQ] [-i inPenalty] [-0 em0] [-1 em1] [-2 em2] [-f ref] <in.bam>
+
+This command identifies target regions by examining the continuity of read depth, computes
+haploid consensus sequences of targets and outputs a SAM with each sequence corresponding
+to a target. When option
+.B -f
+is in use, BAQ will be applied. This command is
+.B only
+designed for cutting fosmid clones from fosmid pool sequencing [Ref. Kitzman et al. (2010)].
.RE
.TP
-.B faidx
-samtools faidx <ref.fasta> [region1 [...]]
+.B phase
+samtools phase [-AF] [-k len] [-b prefix] [-q minLOD] [-Q minBaseQ] <in.bam>
-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.
+Call and phase heterozygous SNPs.
+.B OPTIONS:
+.RS
+.TP 8
+.B -A
+Drop reads with ambiguous phase.
+.TP 8
+.BI -b \ STR
+Prefix of BAM output. When this option is in use, phase-0 reads will be saved in file
+.BR STR .0.bam
+and phase-1 reads in
+.BR STR .1.bam.
+Phase unknown reads will be randomly allocated to one of the two files. Chimeric reads
+with switch errors will be saved in
+.BR STR .chimeric.bam.
+[null]
+.TP
+.B -F
+Do not attempt to fix chimeric reads.
+.TP
+.BI -k \ INT
+Maximum length for local phasing. [13]
+.TP
+.BI -q \ INT
+Minimum Phred-scaled LOD to call a heterozygote. [40]
+.TP
+.BI -Q \ INT
+Minimum base quality to be used in het calling. [13]
+.RE
.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.
+
+.B NOTE:
+Since 0.1.10, the `pileup' command is deprecated by `mpileup'.
.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. 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
-Cap mapping quality at INT [60]
-
+.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 -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.
-
+.B -i
+Only output pileup lines containing indels.
.TP
-.B -l FILE
+.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
-.B -s
-together with
-.B -l
-as in the default format we may not know the mapping quality.
-
-.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.
-
.TP
-.B -g
-Generate genotype likelihood in the binary GLFv3 format. This option
-suppresses -c, -i and -s.
-
+.BI -m \ INT
+Filter reads with flag containing bits in
+.I INT
+[1796]
.TP
-.B -T FLOAT
-The theta parameter (error dependency coefficient) in the maq consensus
-calling model [0.85]
-
+.BI -M \ INT
+Cap mapping quality at INT [60]
.TP
-.B -N INT
+.BI -N \ INT
Number of haplotypes in the sample (>=2) [2]
-
.TP
-.B -r FLOAT
+.BI -r \ FLOAT
Expected fraction of differences between a pair of haplotypes [0.001]
-
-.TP
-.B -I INT
-Phred probability of an indel in sequencing/prep. [40]
-
-.RE
-
-.TP
-.B 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 alignment start from a
-region in the format like `chr10:10,000,000'.
-
-.RE
-
.TP
-.B fixmate
-samtools fixmate <in.nameSrt.bam> <out.bam>
-
-Fill in mate coordinates, ISIZE and mate related flags from a
-name-sorted alignment.
-
+.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 rmdup
-samtools rmdup <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
-.B ONLY
-works with FR orientation and requires ISIZE is correctly set.
-
-.RE
-
+.B -S
+The input file is in SAM.
.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.
-
-.RE
-
+.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.
+.B -s
+together with
+.B -l
+as in the default format we may not know the mapping quality.
.TP
-.B fillmd
-samtools fillmd [-e] <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.
-
-.B OPTIONS:
-.RS
-.TP 8
-.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.
-
+.BI -T \ FLOAT
+The theta parameter (error dependency coefficient) in the maq consensus
+calling model [0.85]
.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 mpileup -ugf ref.fa aln.bam | bcftools view -bvcg - > var.raw.bcf
+ bcftools view var.raw.bcf | vcfutils.pl varFilter -D 100 > var.flt.vcf
+
+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 mpileup
+if mapping quality is overestimated for reads containing excessive
+mismatches. Applying this option usually helps
+.B BWA-short
+but may not other mappers.
+
+.IP o 2
+Generate the consensus sequence for one diploid individual:
+
+ samtools mpileup -uf ref.fa aln.bam | bcftools view -cg - | vcfutils.pl vcf2fq > cns.fq
+
+.IP o 2
+Phase one individual:
+
+ samtools calmd -AEur aln.bam ref.fa | samtools phase -b prefix - > phase.out
+
+The
+.B calmd
+command is used to reduce false heterozygotes around INDELs.
+
+.IP o 2
+Call SNPs and short indels for multiple diploid individuals:
+
+ samtools mpileup -P ILLUMINA -ugf ref.fa *.bam | bcftools view -bcvg - > var.raw.bcf
+ bcftools view var.raw.bcf | vcfutils.pl varFilter -D 2000 > var.flt.vcf
+
+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. The
+.B -P
+option specifies that indel candidates should be collected only from
+read groups with the
+.B @RG-PL
+tag set to
+.IR ILLUMINA .
+Collecting indel candidates from reads sequenced by an indel-prone
+technology may affect the performance of indel calling.
+
+.IP o 2
+Derive the allele frequency spectrum (AFS) on a list of sites from multiple individuals:
+
+ samtools mpileup -Igf 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 -bAr 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 one 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.
-.IP o 2
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' rmdup does not work for single-end data and does not remove
-duplicates across chromosomes. Picard is better.
+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
+Ruan from Beijing Genomics Institute wrote the RAZF library. John
+Marshall and Petr Danecek contribute to the source code and various
+people from the 1000 Genomes Project have contributed to the SAM format
specification.
.SH SEE ALSO
projects / samtools.git / blobdiff