--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/PsiCLASS-1.0.2/samtools-0.1.19/samtools.1	Fri Mar 26 16:52:45 2021 +0000
@@ -0,0 +1,1066 @@
+.TH samtools 1 "15 March 2013" "samtools-0.1.19" "Bioinformatics tools"
+.SH NAME
+.PP
+samtools - Utilities for the Sequence Alignment/Map (SAM) format
+
+bcftools - Utilities for the Binary Call Format (BCF) and VCF
+.SH SYNOPSIS
+.PP
+samtools view -bt ref_list.txt -o aln.bam aln.sam.gz
+.PP
+samtools sort aln.bam aln.sorted
+.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 -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
+.PP
+bcftools index in.bcf
+.PP
+bcftools view in.bcf chr2:100-200 > out.vcf
+.PP
+bcftools view -Nvm0.99 in.bcf > out.vcf 2> out.afs
+
+.SH DESCRIPTION
+.PP
+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 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
+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
+entire alignment file unless it is asked to do so.
+
+.SH SAMTOOLS COMMANDS AND OPTIONS
+
+.TP 10
+.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 10
+.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
+.BI -s \ FLOAT
+Fraction of templates/pairs to subsample; the integer part is treated as the
+seed for the random number generator [-1]
+.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 
+.RB [ \-p 
+.IR chr:pos ]
+.RB [ \-s 
+.IR STR ]
+.RB [ \-d 
+.IR display ] 
+.RI <in.sorted.bam> 
+.RI [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.
+
+.B Options:
+.RS
+.TP 14
+.BI -d \ display
+Output as (H)tml or (C)urses or (T)ext
+.TP
+.BI -p \ chr:pos
+Go directly to this position
+.TP
+.BI -s \ STR
+Display only reads from this sample or read group
+.RE
+
+.TP
+.B mpileup
+samtools mpileup
+.RB [ \-EBugp ]
+.RB [ \-C
+.IR capQcoef ]
+.RB [ \-r
+.IR reg ]
+.RB [ \-f
+.IR in.fa ]
+.RB [ \-l
+.IR list ]
+.RB [ \-M
+.IR capMapQ ]
+.RB [ \-Q
+.IR minBaseQ ]
+.RB [ \-q
+.IR minMapQ ]
+.I in.bam
+.RI [ in2.bam
+.RI [ ... ]]
+
+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.
+
+In the pileup format (without
+.BR -u or -g ),
+each
+line represents a genomic position, consisting of chromosome name,
+coordinate, reference base, read bases, read 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,
+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.
+
+.B Input Options:
+.RS
+.TP 10
+.B -6
+Assume the quality is in the Illumina 1.3+ encoding.
+.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 -b \ FILE
+List of input BAM files, one file per line [null]
+.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 -E
+Extended BAQ computation. This option helps sensitivity especially for MNPs, but may hurt
+specificity a little bit.
+.TP
+.BI -f \ FILE
+The
+.BR faidx -indexed
+reference file in the FASTA format. The file can be optionally compressed by
+.BR razip .
+[null]
+.TP
+.BI -l \ FILE
+BED or position list file containing a list of regions or sites where pileup or BCF should be generated [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]
+.TP
+.B Output Options:
+
+.TP
+.B -D
+Output per-sample read depth
+.TP
+.B -g
+Compute genotype likelihoods and output them in the binary call format (BCF).
+.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.
+
+.TP
+.B Options for Genotype Likelihood Computation (for -g or -u):
+
+.TP
+.BI -e \ INT
+Phred-scaled gap extension sequencing error probability. Reducing
+.I INT
+leads to longer indels. [20]
+.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 \ 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
+Apply -m and -F thresholds per sample to increase sensitivity of calling.
+By default both options are applied to reads pooled from all samples.
+.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]
+.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.
+
+.TP
+.B cat
+samtools cat [-h header.sam] [-o out.bam] <in1.bam> <in2.bam> [ ... ]
+
+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 [-nof] [-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 -n
+Sort by read names rather than by chromosomal coordinates
+.TP
+.B -f
+Use
+.I <out.prefix>
+as the full output path and do not append
+.I .bam
+suffix.
+.TP
+.BI -m \ INT
+Approximately the maximum required memory. [500000000]
+.RE
+
+.TP
+.B merge
+samtools merge [-nur1f] [-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
+.B -1
+Use zlib compression level 1 to comrpess the output
+.TP
+.B -f
+Force to overwrite the output file if present.
+.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
+.B -n
+The input alignments are sorted by read names rather than by chromosomal
+coordinates
+.TP
+.BI -R \ STR
+Merge files in the specified region indicated by
+.I STR
+[null]
+.TP
+.B -r
+Attach an RG tag to each alignment. The tag value is inferred from file names.
+.TP
+.B -u
+Uncompressed BAM output
+.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 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
+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 -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 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 -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
+Compute the BQ tag (without -A) or cap base quality by BAQ (with -A).
+.TP
+.B -E
+Extended BAQ calculation. This option trades specificity for sensitivity, though the
+effect is minor.
+.RE
+
+.TP
+.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 phase
+samtools phase [-AF] [-k len] [-b prefix] [-q minLOD] [-Q minBaseQ] <in.bam>
+
+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
+
+.SH BCFTOOLS COMMANDS AND OPTIONS
+
+.TP 10
+.B view
+.B bcftools view
+.RB [ \-AbFGNQSucgv ]
+.RB [ \-D
+.IR seqDict ]
+.RB [ \-l
+.IR listLoci ]
+.RB [ \-s
+.IR listSample ]
+.RB [ \-i
+.IR gapSNPratio ]
+.RB [ \-t
+.IR mutRate ]
+.RB [ \-p
+.IR varThres ]
+.RB [ \-m
+.IR varThres ]
+.RB [ \-P
+.IR prior ]
+.RB [ \-1
+.IR nGroup1 ]
+.RB [ \-d
+.IR minFrac ]
+.RB [ \-U
+.IR nPerm ]
+.RB [ \-X
+.IR permThres ]
+.RB [ \-T
+.IR trioType ]
+.I in.bcf
+.RI [ region ]
+
+Convert between BCF and VCF, call variant candidates and estimate allele
+frequencies.
+
+.RS
+.TP
+.B Input/Output Options:
+.TP 10
+.B -A
+Retain all possible alternate alleles at variant sites. By default, the view
+command discards unlikely alleles.
+.TP 10
+.B -b
+Output in the BCF format. The default is VCF.
+.TP
+.BI -D \ FILE
+Sequence dictionary (list of chromosome names) for VCF->BCF conversion [null]
+.TP
+.B -F
+Indicate PL is generated by r921 or before (ordering is different).
+.TP
+.B -G
+Suppress all individual genotype information.
+.TP
+.BI -l \ FILE
+List of sites at which information are outputted [all sites]
+.TP
+.B -N
+Skip sites where the REF field is not A/C/G/T
+.TP
+.B -Q
+Output the QCALL likelihood format
+.TP
+.BI -s \ FILE
+List of samples to use. The first column in the input gives the sample names
+and the second gives the ploidy, which can only be 1 or 2. When the 2nd column
+is absent, the sample ploidy is assumed to be 2. In the output, the ordering of
+samples will be identical to the one in
+.IR FILE .
+[null]
+.TP
+.B -S
+The input is VCF instead of BCF.
+.TP
+.B -u
+Uncompressed BCF output (force -b).
+.TP
+.B Consensus/Variant Calling Options:
+.TP 10
+.B -c
+Call variants using Bayesian inference. This option automatically invokes option
+.BR -e .
+.TP
+.BI -d \ FLOAT
+When
+.B -v
+is in use, skip loci where the fraction of samples covered by reads is below FLOAT. [0]
+.TP
+.B -e
+Perform max-likelihood inference only, including estimating the site allele frequency,
+testing Hardy-Weinberg equlibrium and testing associations with LRT.
+.TP
+.B -g
+Call per-sample genotypes at variant sites (force -c)
+.TP
+.BI -i \ FLOAT
+Ratio of INDEL-to-SNP mutation rate [0.15]
+.TP
+.BI -m \ FLOAT
+New model for improved multiallelic and rare-variant calling. Another
+ALT allele is accepted if P(chi^2) of LRT exceeds the FLOAT threshold. The 
+parameter seems robust and the actual value usually does not affect the results
+much; a good value to use is 0.99. This is the recommended calling method. [0]
+.TP
+.BI -p \ FLOAT
+A site is considered to be a variant if P(ref|D)<FLOAT [0.5]
+.TP
+.BI -P \ STR
+Prior or initial allele frequency spectrum. If STR can be
+.IR full ,
+.IR cond2 ,
+.I flat
+or the file consisting of error output from a previous variant calling
+run.
+.TP
+.BI -t \ FLOAT
+Scaled muttion rate for variant calling [0.001]
+.TP
+.BI -T \ STR
+Enable pair/trio calling. For trio calling, option
+.B -s
+is usually needed to be applied to configure the trio members and their ordering.
+In the file supplied to the option
+.BR -s ,
+the first sample must be the child, the second the father and the third the mother.
+The valid values of
+.I STR
+are `pair', `trioauto', `trioxd' and `trioxs', where `pair' calls differences between two input samples, and `trioxd' (`trioxs') specifies that the input
+is from the X chromosome non-PAR regions and the child is a female (male). [null]
+.TP
+.B -v
+Output variant sites only (force -c)
+.TP
+.B Contrast Calling and Association Test Options:
+.TP
+.BI -1 \ INT
+Number of group-1 samples. This option is used for dividing the samples into
+two groups for contrast SNP calling or association test.
+When this option is in use, the following VCF INFO will be outputted:
+PC2, PCHI2 and QCHI2. [0]
+.TP
+.BI -U \ INT
+Number of permutations for association test (effective only with
+.BR -1 )
+[0]
+.TP
+.BI -X \ FLOAT
+Only perform permutations for P(chi^2)<FLOAT (effective only with
+.BR -U )
+[0.01]
+.RE
+
+.TP
+.B index
+.B bcftools index
+.I in.bcf
+
+Index sorted BCF for random access.
+.RE
+
+.TP
+.B cat
+.B bcftools cat
+.I in1.bcf
+.RI [ "in2.bcf " [ ... "]]]"
+
+Concatenate BCF files. The input files are required to be sorted and
+have identical samples appearing in the same order.
+.RE
+.SH SAM FORMAT
+
+Sequence Alignment/Map (SAM) format is TAB-delimited. Apart from the header lines, which are started
+with the `@' symbol, each alignment line consists of:
+
+.TS
+center box;
+cb | cb | cb
+n | l | l .
+Col	Field	Description
+_
+1	QNAME	Query template/pair NAME
+2	FLAG	bitwise FLAG
+3	RNAME	Reference sequence NAME
+4	POS	1-based leftmost POSition/coordinate of clipped sequence
+5	MAPQ	MAPping Quality (Phred-scaled)
+6	CIAGR	extended CIGAR string
+7	MRNM	Mate Reference sequence NaMe (`=' if same as RNAME)
+8	MPOS	1-based Mate POSistion
+9	TLEN	inferred Template LENgth (insert size)
+10	SEQ	query SEQuence on the same strand as the reference
+11	QUAL	query QUALity (ASCII-33 gives the Phred base quality)
+12+	OPT	variable OPTional fields in the format TAG:VTYPE:VALUE
+.TE
+
+.PP
+Each bit in the FLAG field is defined as:
+
+.TS
+center box;
+cb | cb | cb
+l | c | l .
+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
+.TE
+
+where the second column gives the string representation of the FLAG field.
+
+.SH VCF FORMAT
+
+The Variant Call Format (VCF) is a TAB-delimited format with each data line consists of the following fields:
+.TS
+center box;
+cb | cb | cb
+n | l | l .
+Col	Field	Description
+_
+1	CHROM	CHROMosome name
+2	POS	the left-most POSition of the variant
+3	ID	unique variant IDentifier
+4	REF	the REFerence allele
+5	ALT	the ALTernate allele(s), separated by comma
+6	QUAL	variant/reference QUALity
+7	FILTER	FILTers applied
+8	INFO	INFOrmation related to the variant, separated by semi-colon
+9	FORMAT	FORMAT of the genotype fields, separated by colon (optional)
+10+	SAMPLE	SAMPLE genotypes and per-sample information (optional)
+.TE
+
+.PP
+The following table gives the
+.B INFO
+tags used by samtools and bcftools.
+
+.TS
+center box;
+cb | cb | cb
+l | l | l .
+Tag	Format	Description
+_
+AF1	double	Max-likelihood estimate of the site allele frequency (AF) of the first ALT allele
+DP	int	Raw read depth (without quality filtering)
+DP4	int[4]	# high-quality reference forward bases, ref reverse, alternate for and alt rev bases
+FQ	int	Consensus quality. Positive: sample genotypes different; negative: otherwise
+MQ	int	Root-Mean-Square mapping quality of covering reads
+PC2	int[2]	Phred probability of AF in group1 samples being larger (,smaller) than in group2
+PCHI2	double	Posterior weighted chi^2 P-value between group1 and group2 samples
+PV4	double[4]	P-value for strand bias, baseQ bias, mapQ bias and tail distance bias
+QCHI2	int	Phred-scaled PCHI2
+RP	int	# permutations yielding a smaller PCHI2
+CLR	int	Phred log ratio of genotype likelihoods with and without the trio/pair constraint
+UGT	string	Most probable genotype configuration without the trio constraint
+CGT	string	Most probable configuration with the trio constraint
+VDB	float	Tests variant positions within reads. Intended for filtering RNA-seq artifacts around splice sites
+RPB	float	Mann-Whitney rank-sum test for tail distance bias
+HWE	float	Hardy-Weinberg equilibrium test, Wigginton et al., PMID: 15789306
+.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
+Call somatic mutations from a pair of samples:
+
+  samtools mpileup -DSuf ref.fa aln.bam | bcftools view -bvcgT pair - > var.bcf
+
+In the output INFO field,
+.I CLR
+gives the Phred-log ratio between the likelihood by treating the
+two samples independently, and the likelihood by requiring the genotype to be identical.
+This
+.I CLR
+is effectively a score measuring the confidence of somatic calls. The higher the better.
+
+.IP o 2
+Call de novo and somatic mutations from a family trio:
+
+  samtools mpileup -DSuf ref.fa aln.bam | bcftools view -bvcgT pair -s samples.txt - > var.bcf
+
+File
+.I samples.txt
+should consist of three lines specifying the member and order of samples (in the order of child-father-mother).
+Similarly,
+.I CLR
+gives the Phred-log likelihood ratio with and without the trio constraint.
+.I UGT
+shows the most likely genotype configuration without the trio constraint, and
+.I CGT
+gives the most likely genotype configuration satisfying the trio constraint.
+
+.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.
+
+Note that there is a new calling model which can be invoked by
+
+    bcftools view -m0.99  ...
+
+which fixes some severe limitations of the default method.
+
+For filtering, best results seem to be achieved by first applying the
+.IR SnpGap
+filter and then applying some machine learning approach
+
+    vcf-annotate -f SnpGap=n
+    vcf filter ...
+
+Both can be found in the 
+.B vcftools
+and
+.B htslib
+package (links below).
+
+.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
+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. 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
+.PP
+Samtools website: <http://samtools.sourceforge.net>
+.br
+Samtools latest source: <https://github.com/samtools/samtools>
+.br
+VCFtools website with stable link to VCF specification: <http://vcftools.sourceforge.net>
+.br
+HTSlib website: <https://github.com/samtools/htslib>