16 <param name="probability" type="float" size="5" label="Probability (between 0 and 1) that any given read will be kept" help="specify 1 to keep all reads, 0.1 to keep 10% of the reads" value="1" />
37 Randomly down-sample a SAM or BAM file to retain a random subset of the reads. Mate-pairs are either both kept or both discarded. Reads marked as not primary alignments are all discarded. Each read is given a probability P of being retained - results with the exact same input in the same order and with the same value for RANDOM_SEED will produce the same results.
51 Many SAM/BAM files produced externally and uploaded to Galaxy do not fully conform to SAM/BAM specifications. Galaxy deals with this by using the **LENIENT**