Self-explanatory. Useful for example for preserving unmapped reads, operating on aligned reads, and then adding the unmapped reads back to create a "lossless" bam. Command could be run serially if finer control is desired, e.g. permanently discard secondary alignments and preserve unmapped reads only.
Self-explanatory. Useful for example for preserving unmapped reads, operating on aligned reads, and then adding the unmapped reads back to create a "lossless" bam. Command could be run serially if finer control is desired, e.g. permanently discard secondary alignments and preserve unmapped reads only.