-.TH samtools 1 "28 January 2009" "samtools-0.1.2" "Bioinformatics tools"
+.TH samtools 1 "21 May 2009" "samtools-0.1.4" "Bioinformatics tools"
.SH NAME
.PP
samtools - Utilities for the Sequence Alignment/Map (SAM) format
.SH SYNOPSIS
.PP
-samtools import ref_list.txt aln.sam.gz aln.bam
+samtools view -bt ref_list.txt -o aln.bam aln.sam.gz
.PP
samtools sort aln.bam aln.sorted
.PP
.B import
samtools import <in.ref_list> <in.sam> <out.bam>
-Convert alignments in SAM format to BAM format. File
-.I <in.ref_list>
-is TAB-delimited. Each line must contain the reference name and the
-length of the reference, one line for each distinct reference;
-additional fields are ignored. This file also defines the order of the
-reference sequences in sorting. File
-.I <in.sam>
-can be optionally compressed by zlib or gzip. A single hyphen is
-recognized as stdin or stdout, depending on the context. If you run
-`samtools faidx <ref.fa>', the resultant index file
-.I <ref.fa>.fai
-can be used as this
-.I <in.ref_list>
-file.
+Since 0.1.4, this command is an alias of:
+
+samtools view -bt <in.ref_list> -o <out.bam> <in.sam>
.TP
.B sort
.TP
.B view
-samtools view [-b] <in.bam> [region1 [...]]
+samtools view [-bhHS] [-t in.refList] [-o output] [-f reqFlag] [-F
+skipFlag] [-q minMapQ] <in.bam> [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
.TP 8
.B -b
Output in the BAM format.
+.TP
+.B -h
+Include the header in the output.
+.TP
+.B -H
+Output the header only.
+.TP
+.B -S
+Input is in SAM. If @SQ header lines are absent, the
+.B `-t'
+option is required.
+.TP
+.B -t FILE
+This file is TAB-delimited. Each line must contain the reference name
+and the length of the reference, one line for each distinct reference;
+additional fields are ignored. This file also defines the order of the
+reference sequences in sorting. If you run `samtools faidx <ref.fa>',
+the resultant index file
+.I <ref.fa>.fai
+can be used as this
+.I <in.ref_list>
+file.
+.TP
+.B -o FILE
+Output file [stdout]
+.TP
+.B -f INT
+Only output alignments with all bits in INT present in the FLAG
+field. INT can be in hex in the format of /^0x[0-9A-F]+/ [0]
+.TP
+.B -F INT
+Skip alignments with bits present in INT [0]
+.TP
+.B -q INT
+Skip alignments with MAPQ smaller than INT [0]
.RE
.TP
there is an insertion between this reference position and the next
reference position. The length of the insertion is given by the integer
in the pattern, followed by the inserted sequence. Similarly, a pattern
-`-[0-9]+[ACGTNacgtn]+' represents a deletion from the reference. Also at
+`-[0-9]+[ACGTNacgtn]+' represents a deletion from the reference. The
+deleted bases will be presented as `*' in the following lines. Also at
the read base column, a symbol `^' marks the start of a read segment
which is a contiguous subsequence on the read separated by `N/S/H' CIGAR
operations. The ASCII of the character following `^' minus 33 gives the
If option
.B -c
-is applied, the consensus base, consensus quality, SNP quality and
-maximum 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, top two high-scoring ins/del sequences, the
-number of reads strongly supporting the first indel, the number of reads
-strongly supporting the second indel, the number of reads that confer
-little information on distinguishing indels and the number of reads that
-contain indels different from the top two ones.
+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.
.B OPTIONS:
.RS
.TP
.B -c
-Call the consensus sequnce using MAQ consensus model. Options
+Call the consensus sequence using MAQ consensus model. Options
.B -T,
.B -N
and
.TP
.B -g
-Generate genotype likelihood in the binary GLFv2 format. This option
+Generate genotype likelihood in the binary GLFv3 format. This option
suppresses -c, -i and -s.
.TP
.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>
+
+Generate the MD tag. If the MD tag is already present, this command will
+give a warning if the MD tag generated is different from the existing
+tag.
+
+.B OPTIONS:
+.RS
+.TP 8
+.B -e
+Convert a the read base to = if it is identical to the aligned reference
+base. Indel caller does not support the = bases at the moment.
+
+.RE
+
.SH SAM FORFAM
.SH LIMITATIONS
.PP
.IP o 2
-In general, more testing is needed to ensure there is no severe bug.
-.IP o 2
-Reference sequence names and lengths are not acquired from the BAM/SAM header.
+Unaligned words used in bam_import.c, bam_endian.h, bam.c and bam_aux.c.
.IP o 2
-CIGAR operations N and P may not be properly handled.
+CIGAR operation P is not properly handled at the moment.
.IP o 2
-There is a small memory leak in the viewer.
+The text viewer mysteriously crashes in a very rare case.
.SH AUTHOR
.PP
-Heng Li from the Sanger Institute is the author of the C version of
-samtools. Bob Handsaker from the Broad Institute implemented the BGZF
-library and Jue Ruan from Beijing Genomics Institute wrote the RAZF
-library. Various people in the 1000Genomes Project contributed to the
-SAM format specification.
+Heng Li from the Sanger Institute wrote the C version of samtools. Bob
+Handsaker from the Broad Institute implemented the BGZF library and Jue
+Ruan from Beijing Genomics Institute wrote the RAZF library. Various
+people in the 1000Genomes Project contributed to the SAM format
+specification.
.SH SEE ALSO
.PP
projects / samtools.git / blobdiff