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

NAME

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

SYNOPSIS

       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,  -N,  -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, -B, --add-flags, and --remove-flags 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 usage.

       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, --bam Output in the BAM format.

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

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

-u, --uncompressed
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, --with-header
Include the header in the output.

-H, --header-only
Output the header only.

--no-header
When producing SAM format, output alignment records but not headers. This is
the default; the option can be used to reset the effect of -h/-H.

-c, --count
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.

-?, --help
Output long help and exit immediately.

-o FILE, --output FILE
Output to FILE [stdout].

-U FILE, --unoutput FILE, --output-unselected 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, --fai-reference 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, --reference 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, if the reference file is local.

If the reference file is not local, but is accessed instead via an https://,
s3:// or other URL, the index file will need to be supplied by the server
alongside the reference. It is possible to have the reference and index files
in different locations by supplying both to this option separated by the string
"##idx##", for example:

-T ftp://x.com/ref.fa##idx##ftp://y.com/index.fa.fai

However, note that only the location of the reference will be stored in the
output file header. If this method is used to make CRAM files, the cram reader
may not be able to find the index, and may not be able to decode the file unless
it can get the references it needs using a different method.

-L FILE, --target-file FILE, --targets-file FILE
Only output alignments overlapping the input BED FILE [null].

-M, --use-index
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.

--region-file FILE, --regions-file FILE
Use an index and multi-region iterator to only output alignments overlapping the
input BED FILE. Equivalent to -M -L FILE or --use-index --target-file FILE.

-N FILE, --qname-file FILE
Output only alignments with read names listed in FILE.

-r STR, --read-group 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, --read-group-file 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 STR1[:STR2], --tag STR1[:STR2]
Only output alignments with tag STR1 and associated value STR2, which can be a
string or an integer [null]. The value can be omitted, in which case only the
tag is considered.

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

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

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

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

-e STR, --expr STR
Only include alignments that match the filter expression STR. The syntax for
these expressions is described in the main samtools(1) man page under the FILTER
EXPRESSIONS heading.

-f FLAG, --require-flags FLAG
Only output alignments with all bits set in FLAG present in the FLAG field.
FLAG can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/), in
octal by beginning with `0' (i.e. /^0[0-7]+/), as a decimal number not beginning
with '0' or as a comma-separated list of flag names.

For a list of flag names see samtools-flags(1).

-F FLAG, --excl-flags FLAG, --exclude-flags FLAG
Do not output alignments with any bits set in FLAG present in the FLAG field.
FLAG can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/), in
octal by beginning with `0' (i.e. /^0[0-7]+/), as a decimal number not beginning
with '0' or as a comma-separated list of flag names.

-G FLAG 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. FLAG can be specified in hex by beginning with `0x' (i.e. /^0x[0-9A-F]+/),
in octal by beginning with `0' (i.e. /^0[0-7]+/), as a decimal number not
beginning with '0' or as a comma-separated list of flag names.

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

-B, --remove-B
Collapse the backward CIGAR operation.

--add-flags FLAG
Adds flag(s) to read. FLAG can be specified in hex by beginning with `0x' (i.e.
/^0x[0-9A-F]+/), in octal by beginning with `0' (i.e. /^0[0-7]+/), as a decimal
number not beginning with '0' or as a comma-separated list of flag names.

--remove-flags FLAG
Remove flag(s) from read. FLAG is specified in the same way as with the --add-
flags option.

--subsample FLOAT
Output only a proportion of the input alignments, as specified by 0.0 ≤ FLOAT ≤
1.0, which gives the fraction of templates/pairs to be kept. 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.

--subsample-seed INT
Subsampling seed used to influence 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. [0]

-s FLOAT Subsampling shorthand option: -s INT.FRAC is equivalent to --subsample-seed INT
--subsample 0.FRAC.

-@ INT, --threads 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, --customized-index
Include customized index file as a part of arguments. See EXAMPLES section for
sample of usage.

--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 -bo aln.bam aln.sam

If @SQ lines are absent:

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

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 -o aln.cram aln.bam

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 arguments.

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

o Remove the actions of samtools markdup. Clear the duplicate flag and remove the dt tag,
keep the header.

samtools view -h --remove-flags DUP -x dt -o /data_folder/dat.no_dup_markings.bam /data_folder/data.bam

AUTHOR