Fractional (Raw Reads) Downsampling
DRAGEN can subsample a random, fractional percentage of reads from an input file using the fractional downsampler. You can use downsampling to subsample data sets in order to simulate different amounts of sequencing. DRAGEN randomly subsamples reads from primary analysis without any modification (e.g. no trimming, no filtering, etc.).
To enable fractional downsampling, set the --enable-fractional-down-sampler
command line option to true
.
Any valid sequencing data format that is compatible with the DRAGEN Host Software can be used. For more information on compatible input options, see Input Options.
Command Line Options
In addition to enabling the fractional downsampling command line option, you must set the subsample fraction to downsample. To set the subsample fraction, use --down-sampler-normal-subsample
and/or --down-sampler-tumor-subsample
depending on the input files.
You can also specify a seed using --down-sampler-random-seed
to generate different subsamples of the input data set.
Option | Description |
---|---|
| Set to |
| Specify the fraction of reads to keep as a subsample of normal input data. The default value is 1.0 (100%). |
| Specify the fraction of reads to keep as a subsample of tumor input data. The default value is 1.0 (100%). |
| Specify the random seed for different runs of the same input data. The default value is 42. |
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