rename iterf as iter

[samtools.git] / samtools.1

diff --git a/samtools.1 b/samtools.1
index 7b50ef997de2357fed193ff54dcd151c6cb31cee..366a5630ececd0956b6225ad44bbc5d5fb7f087c 100644 (file)
--- 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 <in.nameSrt.bam> <out.bam>
@@ -341,8 +346,6 @@ This command
 .B ONLY
 works with FR orientation and requires ISIZE is correctly set.
 
-.RE
-
 .TP
 .B rmdupse
 samtools rmdupse <input.srt.bam> <out.bam>
@@ -350,8 +353,6 @@ 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
-
 .TP
 .B fillmd
 samtools fillmd [-e] <aln.bam> <ref.fasta>