X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=samtools.git;a=blobdiff_plain;f=samtools.1;h=98ce9d04d92d3f38c36ef8809962ea155359c38f;hp=c71fc879d8c5f590f71a90cd27f09573b1520e62;hb=b301e959d73eee0955c57004f344f17af00703f4;hpb=8a8212c76299ff302cdd41be704d8e0308bd2b1b diff --git a/samtools.1 b/samtools.1 index c71fc87..98ce9d0 100644 --- a/samtools.1 +++ b/samtools.1 @@ -1,7 +1,9 @@ -.TH samtools 1 "21 April 2011" "samtools-0.1.16" "Bioinformatics tools" +.TH samtools 1 "05 July 2011" "samtools-0.1.17" "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 @@ -23,6 +25,12 @@ samtools pileup -vcf ref.fasta aln.sorted.bam 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 -vc in.bcf > out.vcf 2> out.afs .SH DESCRIPTION .PP @@ -43,7 +51,7 @@ 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 +.SH SAMTOOLS COMMANDS AND OPTIONS .TP 10 .B view @@ -137,15 +145,56 @@ 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 [...]] +.B samtools mpileup +.RB [ \-EBug ] +.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. -.B OPTIONS: +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 @@ -155,6 +204,9 @@ 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 @@ -167,24 +219,57 @@ 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] +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 @@ -198,9 +283,6 @@ is modeled as .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 . @@ -217,25 +299,6 @@ Comma dilimited list of platforms (determined by 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 @@ -485,139 +548,174 @@ Minimum Phred-scaled LOD to call a heterozygote. [40] Minimum base quality to be used in het calling. [13] .RE -.TP -.B 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] -| +.SH BCFTOOLS COMMANDS AND OPTIONS -Print the alignment in the pileup format. In the pileup format, 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. - -If option -.B -c -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'. +.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 [ \-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. -.B OPTIONS: .RS +.TP +.B Input/Output Options: .TP 10 -.B -B -Disable the BAQ computation. See the -.B mpileup -command for details. +.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 -.B -c -Call the consensus sequence. Options -.BR -T ", " -N ", " -I " and " -r -are only effective when -.BR -c " or " -g -is in use. +.BI -D \ FILE +Sequence dictionary (list of chromosome names) for VCF->BCF conversion [null] .TP -.BI -C \ INT -Coefficient for downgrading the mapping quality of poorly mapped -reads. See the -.B mpileup -command for details. [0] +.B -F +Indicate PL is generated by r921 or before (ordering is different). .TP -.BI -d \ INT -Use the first -.I NUM -reads in the pileup for indel calling for speed up. Zero for unlimited. [1024] +.B -G +Suppress all individual genotype information. .TP -.BI -f \ FILE -The reference sequence in the FASTA format. Index file -.I FILE.fai -will be created if -absent. +.BI -l \ FILE +List of sites at which information are outputted [all sites] .TP -.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. +.B -N +Skip sites where the REF field is not A/C/G/T .TP -.B -i -Only output pileup lines containing indels. +.B -Q +Output the QCALL likelihood format .TP -.BI -I \ INT -Phred probability of an indel in sequencing/prep. [40] +.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 -.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 +The input is VCF instead of BCF. .TP -.BI -m \ INT -Filter reads with flag containing bits in -.I INT -[1796] +.B -u +Uncompressed BCF output (force -b). .TP -.BI -M \ INT -Cap mapping quality at INT [60] +.B Consensus/Variant Calling Options: +.TP 10 +.B -c +Call variants using Bayesian inference. This option automatically invokes option +.BR -e . .TP -.BI -N \ INT -Number of haplotypes in the sample (>=2) [2] +.BI -d \ FLOAT +When +.B -v +is in use, skip loci where the fraction of samples covered by reads is below FLOAT. [0] .TP -.BI -r \ FLOAT -Expected fraction of differences between a pair of haplotypes [0.001] +.B -e +Perform max-likelihood inference only, including estimating the site allele frequency, +testing Hardy-Weinberg equlibrium and testing associations with LRT. .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. +.B -g +Call per-sample genotypes at variant sites (force -c) .TP -.B -S -The input file is in SAM. +.BI -i \ FLOAT +Ratio of INDEL-to-SNP mutation rate [0.15] .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 -is in SAM format; otherwise it assumes in BAM format. +.BI -p \ FLOAT +A site is considered to be a variant if P(ref|D)