From 412046944a79dd0d3af6ac77e234f571e7624499 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Tue, 7 Jul 2009 00:13:32 +0000 Subject: [PATCH] update documentation --- samtools.1 | 56 +++++++++++++++++++++++++++++++++++++++++++++--------- 1 file changed, 47 insertions(+), 9 deletions(-) diff --git a/samtools.1 b/samtools.1 index c4bd77e..d111aa6 100644 --- a/samtools.1 +++ b/samtools.1 @@ -1,4 +1,4 @@ -.TH samtools 1 "21 May 2009" "samtools-0.1.4" "Bioinformatics tools" +.TH samtools 1 "6 July 2009" "samtools-0.1.5" "Bioinformatics tools" .SH NAME .PP samtools - Utilities for the Sequence Alignment/Map (SAM) format @@ -27,7 +27,20 @@ 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 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. + .SH COMMANDS AND OPTIONS + .TP 10 .B import samtools import @@ -85,15 +98,16 @@ will be created. .TP .B view -samtools view [-bhHS] [-t in.refList] [-o output] [-f reqFlag] [-F -skipFlag] [-q minMapQ] [region1 [...]] +samtools view [-bhuHS] [-t in.refList] [-o output] [-f reqFlag] [-F +skipFlag] [-q minMapQ] [-l library] [-r readGroup] | [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 with the specified regions will be output. An +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'. +format: `chr2', `chr2:1000000' or `chr2:1,000,000-2,000,000'. The coordinate +is 1-based. .B OPTIONS: .RS @@ -101,6 +115,10 @@ format: `chr2', `chr2:1000000' or `chr2:1,000,000-2,000,000'. .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. +.TP .B -h Include the header in the output. .TP @@ -135,6 +153,12 @@ 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] .RE .TP @@ -155,7 +179,7 @@ format. .TP .B pileup samtools pileup [-f in.ref.fasta] [-t in.ref_list] [-l in.site_list] -[-iscg] [-T theta] [-N nHap] [-r pairDiffRate] +[-iscgS2] [-T theta] [-N nHap] [-r pairDiffRate] | Print the alignment in the pileup format. In the pileup format, each line represents a genomic position, consisting of chromosome name, @@ -195,6 +219,10 @@ allele and # reads containing indels different from the top two alleles. 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 .B -i Only output pileup lines containing indels. @@ -206,6 +234,10 @@ The reference sequence in the FASTA format. Index file will be created if absent. +.TP +.B -M INT +Cap mapping quality at INT [60] + .TP .B -t FILE List of reference names ane sequence lengths, in the format described @@ -230,11 +262,14 @@ as in the default format we may not know the mapping quality. .B -c Call the consensus sequence using MAQ consensus model. Options .B -T, -.B -N +.B -N, +.B -I and .B -r are only effective when .B -c +or +.B -g is in use. .TP @@ -255,6 +290,10 @@ Number of haplotypes in the sample (>=2) [2] .B -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 @@ -314,8 +353,7 @@ base. Indel caller does not support the = bases at the moment. .RE - -.SH SAM FORFAM +.SH SAM FORMAT SAM is TAB-delimited. Apart from the header lines, which are started with the `@' symbol, each alignment line consists of: -- 2.39.2