### DownsampleSam

USAGE: DownsampleSam [options]

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. 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.

Option | Description
--- | ---
INPUT=File | The input SAM or BAM file to downsample. Required.
OUTPUT=File | The output, downsampled, SAM or BAM file to write. Required.
RANDOM_SEED=Long | Random seed to use if reproducibilty is desired. Default value: 1. This option can be set to 'null' to clear the default value.
PROBABILITY=Double | The probability of keeping any individual read, between 0 and 1. Default value: 1.0. This option can be set to 'null' to clear the default value.