samtools-view.cwl is developed for CWL consortium Usage: samtools view [options] <in.bam>|<in.sam>|<in.cram> [region ...]

Options: -b output BAM -C output CRAM (requires -T) -1 use fast BAM compression (implies -b) -u uncompressed BAM output (implies -b) -h include header in SAM output -H print SAM header only (no alignments) -c print only the count of matching records -o FILE output file name [stdout] -U FILE output reads not selected by filters to FILE [null] -t FILE FILE listing reference names and lengths (see long help) [null] -T FILE reference sequence FASTA FILE [null] -L FILE only include reads overlapping this BED FILE [null] -r STR only include reads in read group STR [null] -R FILE only include reads with read group listed in FILE [null] -q INT only include reads with mapping quality >= INT [0] -l STR only include reads in library STR [null] -m INT only include reads with number of CIGAR operations consuming query sequence >= INT [0] -f INT only include reads with all bits set in INT set in FLAG [0] -F INT only include reads with none of the bits set in INT set in FLAG [0] -x STR read tag to strip (repeatable) [null] -B collapse the backward CIGAR operation -s FLOAT integer part sets seed of random number generator [0]; rest sets fraction of templates to subsample [no subsampling] -@ INT number of BAM compression threads [0]