Prints alignments in the specified input alignment file.

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, -r, -R, -q, -l, -m, -f, and -F options filter the alignments that will be included in the output to only those alignments that match certain criteria.

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

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

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

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).

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].

-r STR Only output alignments in read group STR [null].

-R FILE Output alignments in read groups 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].

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

-B Collapse the backward CIGAR operation.

-s FLOAT Integer part is used to seed the random number generator [0]. Part after the decimal point sets the fraction of templates/pairs to subsample [no subsampling].

-@ 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.