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Added resource usage section to the GermlineCNVCaller java doc. #8064

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Mar 28, 2023
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Added resource usage section to the GermlineCNVCaller java doc. #8064

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26 changes: 26 additions & 0 deletions src/main/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCaller.java
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Expand Up @@ -97,6 +97,32 @@
* https://theano-pymc.readthedocs.io/en/latest/library/config.html</a>.
* </p>
*
* <h3>Resource usage</h3>
*
* <p>Runtime and memory usage for {@link GermlineCNVCaller} can be impacted by (1) the number of input samples, (2) the
* number of intervals, (3) the highest allowed copy-number state (set using the {@code max-copy-number} argument),
* (4) the number of bias factors (set using the {@code max-bias-factors} argument), and convergence criteria.</p>
*
* <p>We recommend running {@link GermlineCNVCaller} in COHORT mode for approximately 200 samples at a time, processing
* between 5k to 12.5k intervals, and {@code max-copy-number} set to 5 across all analyses. For 200 samples and
* 5k intervals, approximately 16GB of memory should be enough to optimize memory usage; for the same
* analysis at 12.5k intervals, we recommend 32GB of memory. Runtimes are on the order of a few hours.</p>
*
* <p>Note that {@link GermlineCNVCaller} can be run on larger interval sets by scattering them into smaller "shards."
* The shards can subsequently be merged together by {@link PostprocessGermlineCNVCalls} tool. In cloud
* and HPC environments, the tool can then process each shard in parallel within a single job.</p>
*
* <p>By default, {@link GermlineCNVCaller} will attempt to use all CPU cores accessible to it within the runtime
* environment. Two environment variables - <code>MKL_NUM_THREADS</code> and <code>OMP_NUM_THREADS</code> - control the
* parallelism of the underlying linear algebra libraries.</p>
*
* <p>Runtime is also affected by how fast the inference procedure converges. There are multiple tool arguments that can
* be used to set convergence criteria that could speed up this convergence, including but not limited to
* {@code caller-update-convergence-threshold}, {@code convergence-snr-averaging-window},
* {@code convergence-snr-countdown-window}, and {@code convergence-snr-trigger-threshold}. However, modifying these
* arguments from the default settings might affect the final results, so please exercise caution if
* including any of these arguments.</p>
*
* <h3>Tool run modes</h3>
* <dl>
* <dt>COHORT mode:</dt>
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