Ubuntu Manpage: samtools view - views and converts SAM/BAM/CRAM files

NAME

       samtools view - views and converts SAM/BAM/CRAM files

SYNOPSIS

       view samtools view [options] in.sam|in.bam|in.cram [region...]

DESCRIPTION

       With  no  options  or  regions specified, prints all alignments in the specified input alignment file (in
       SAM, BAM, or CRAM format) to standard output in SAM format (with no header).

       You may specify one or more space-separated region specifications after the input  filename  to  restrict
       output  to  only  those  alignments  which  overlap the specified region(s). Use of region specifications
       requires a coordinate-sorted and indexed input file (in BAM or CRAM format).

       The -b, -C, -1, -u, -h, -H, and -c options change the output format from the default of  headerless  SAM,
       and the -o and -U options set the output file name(s).

       The  -t  and  -T options provide additional reference data. One of these two options is required when SAM
       input does not contain @SQ headers, and the -T option is required whenever writing CRAM output.

       The -L, -M, -r, -R, -d, -D, -s, -q, -l, -m, -f, -F, and -G options filter the  alignments  that  will  be
       included in the output to only those alignments that match certain criteria.

       The -x and -B options modify the data which is contained in each alignment.

       The  -X  option can be used to allow user to specify customized index file location(s) if the data folder
       does not contain any index file. See EXAMPLES section for sample of useage.

       Finally, the -@ option can be used to allocate additional threads to be used for compression, and the  -?
       option requests a long help message.

       REGIONS:
              Regions can be specified as: RNAME[:STARTPOS[-ENDPOS]] and all position coordinates are 1-based.

              Important  note:  when multiple regions are given, some alignments may be output multiple times if
              they overlap more than one of the specified regions.

              Examples of region specifications:

              chr1      Output all alignments mapped to the reference sequence named `chr1' (i.e. @SQ SN:chr1).

              chr2:1000000
                        The region on chr2 beginning at base position 1,000,000 and ending at  the  end  of  the
                        chromosome.

              chr3:1000-2000
                        The  1001bp  region on chr3 beginning at base position 1,000 and ending at base position
                        2,000 (including both end positions).

              '*'       Output the unmapped reads at the end of the file.  (This does not include  any  unmapped
                        reads placed on a reference sequence alongside their mapped mates.)

              .         Output  all  alignments.   (Mostly unnecessary as not specifying a region at all has the
                        same effect.)

OPTIONS

-b Output in the BAM format.

-C Output in the CRAM format (requires -T).

-1 Enable fast BAM compression (implies -b).

-u Output uncompressed BAM. This option saves time spent on compression/decompression and is thus
preferred when the output is piped to another samtools command.

-h Include the header in the output.

-H Output the header only.

-c Instead of printing the alignments, only count them and print the total number. All filter
options, such as -f, -F, and -q, are taken into account.

-? Output long help and exit immediately.

-o FILE Output to FILE [stdout].

-U FILE Write alignments that are not selected by the various filter options to FILE. When this option
is used, all alignments (or all alignments intersecting the regions specified) are written to
either the output file or this file, but never both.

-t FILE A tab-delimited FILE. Each line must contain the reference name in the first column and the
length of the reference in the second column, with one line for each distinct reference. Any
additional fields beyond the second column are ignored. This file also defines the order of the
reference sequences in sorting. If you run: `samtools faidx <ref.fa>', the resulting index file
<ref.fa>.fai can be used as this FILE.

-T FILE A FASTA format reference FILE, optionally compressed by bgzip and ideally indexed by samtools
faidx. If an index is not present, one will be generated for you.

-L FILE Only output alignments overlapping the input BED FILE [null].

-M Use the multi-region iterator on the union of a BED file and command-line region arguments.
This avoids re-reading the same regions of files so can sometimes be much faster. Note this
also removes duplicate sequences. Without this a sequence that overlaps multiple regions
specified on the command line will be reported multiple times. The usage of a BED file is
optional and its path has to be preceded by -L option.

-r STR Output alignments in read group STR [null]. Note that records with no RG tag will also be
output when using this option. This behaviour may change in a future release.

-R FILE Output alignments in read groups listed in FILE [null]. Note that records with no RG tag will
also be output when using this option. This behaviour may change in a future release.

-d STR:STR
Only output alignments with tag STR and associated value STR [null].

-D STR:FILE
Only output alignments with tag STR and associated values listed in FILE [null].

-q INT Skip alignments with MAPQ smaller than INT [0].

-l STR Only output alignments in library STR [null].

-m INT Only output alignments with number of CIGAR bases consuming query sequence ≥ INT [0]

-f INT Only output alignments with all bits set in INT present in the FLAG field. INT can be
specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0'
(i.e. /^0[0-7]+/) [0].

-F INT Do not output alignments with any bits set in INT present in the FLAG field. INT can be
specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0'
(i.e. /^0[0-7]+/) [0].

-G INT Do not output alignments with all bits set in INT present in the FLAG field. This is the
opposite of -f such that -f12 -G12 is the same as no filtering at all. INT can be specified in
hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/) or in octal by beginning with `0' (i.e.
/^0[0-7]+/) [0].

-x STR Read tag to exclude from output (repeatable) [null]

-B Collapse the backward CIGAR operation.

-s FLOAT Output only a proportion of the input alignments. This subsampling acts in the same way on all
of the alignment records in the same template or read pair, so it never keeps a read but not
its mate.

The integer and fractional parts of the -s INT.FRAC option are used separately: the part after
the decimal point sets the fraction of templates/pairs to be kept, while the integer part is
used as a seed that influences which subset of reads is kept.

When subsampling data that has previously been subsampled, be sure to use a different seed
value from those used previously; otherwise more reads will be retained than expected.

-@ INT Number of BAM compression threads to use in addition to main thread [0].

-S Ignored for compatibility with previous samtools versions. Previously this option was required
if input was in SAM format, but now the correct format is automatically detected by examining
the first few characters of input.

-X Include customized index file as a part of arugments. See EXAMPLES section for sample of
useage.

--no-PG Do not add a @PG line to the header of the output file.

EXAMPLES

o Import SAM to BAM when @SQ lines are present in the header:

samtools view -bS aln.sam > aln.bam

If @SQ lines are absent:

samtools faidx ref.fa
samtools view -bt ref.fa.fai aln.sam > aln.bam

where ref.fa.fai is generated automatically by the faidx command.

o Convert a BAM file to a CRAM file using a local reference sequence.

samtools view -C -T ref.fa aln.bam > aln.cram

o Convert a BAM file to a CRAM with NM and MD tags stored verbatim rather than calculating on the fly
during CRAM decode, so that mixed data sets with MD/NM only on some records, or NM calculated using
different definitions of mismatch, can be decoded without change. The second command demonstrates how
to decode such a file. The request to not decode MD here is turning off auto-generation of both MD and
NM; it will still emit the MD/NM tags on records that had these stored verbatim.

samtools view -C --output-fmt-option store_md=1 --output-fmt-option store_nm=1 -o aln.cram aln.bam
samtools view --input-fmt-option decode_md=0 -o aln.new.bam aln.cram

o An alternative way of achieving the above is listing multiple options after the --output-fmt or -O
option. The commands below are equivalent to the two above.

samtools view -O cram,store_md=1,store_nm=1 -o aln.cram aln.bam
samtools view --input-fmt cram,decode_md=0 -o aln.new.bam aln.cram

o Include customized index file as a part of arugments.

samtools view [options] -X /data_folder/data.bam /index_folder/data.bai chrM:1-10

o Output alignments in read group grp2 (records with no RG tag will also be in the output).

samtools view -r grp2 -o /data_folder/data.rg2.bam /data_folder/data.bam

o Only keep reads with tag BC and were the barcode matches the barcodes listed in the barcode file.

samtools view -D BC:barcodes.txt -o /data_folder/data.barcodes.bam /data_folder/data.bam

o Only keep reads with tag RG and read group grp2. This does almost the same than -r grp2 but will not
keep records without the RG tag.

samtools view -d RG:grp2 -o /data_folder/data.rg2_only.bam /data_folder/data.bam

AUTHOR