X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=samtools.1;h=366a5630ececd0956b6225ad44bbc5d5fb7f087c;hb=a958954399757774ee26bfcf0b5b95e9ec9b62f4;hp=7b50ef997de2357fed193ff54dcd151c6cb31cee;hpb=521aa49c29217a0398ff5e186072df97cf9d80c4;p=samtools.git diff --git a/samtools.1 b/samtools.1 index 7b50ef9..366a563 100644 --- a/samtools.1 +++ b/samtools.1 @@ -1,4 +1,4 @@ -.TH samtools 1 "6 July 2009" "samtools-0.1.5" "Bioinformatics tools" +.TH samtools 1 "10 November 2009" "samtools-0.1.7" "Bioinformatics tools" .SH NAME .PP samtools - Utilities for the Sequence Alignment/Map (SAM) format @@ -18,6 +18,8 @@ samtools faidx ref.fasta .PP samtools pileup -f ref.fasta aln.sorted.bam .PP +samtools mpileup -f ref.fasta -r chr3:1,000-2,000 in1.bam in2.bam +.PP samtools tview aln.sorted.bam ref.fasta .SH DESCRIPTION @@ -123,8 +125,9 @@ 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 @@ -220,14 +223,18 @@ 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 @@ -322,8 +329,6 @@ 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 @@ -341,8 +346,6 @@ This command .B ONLY works with FR orientation and requires ISIZE is correctly set. -.RE - .TP .B rmdupse samtools rmdupse @@ -350,8 +353,6 @@ samtools rmdupse Remove potential duplicates for single-ended reads. This command will treat all reads as single-ended even if they are paired in fact. -.RE - .TP .B fillmd samtools fillmd [-e]