-.TH samtools 1 "2 September 2009" "samtools-0.1.6" "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
.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
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
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