samtools view [options] in.sam|in.bam|in.cram [region...] 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, -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. Finally, the -@ option can be used to allocate additional threads to be used for compression, and the -? option requests a long help message.
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