-.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
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
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.
.B OPTIONS:
.RS
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>
.B ONLY
works with FR orientation and requires ISIZE is correctly set.
-.RE
-
.TP
.B rmdupse
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>