diff --git a/src/main/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCaller.java b/src/main/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCaller.java index 0ed49977bee..418e95296ae 100644 --- a/src/main/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCaller.java +++ b/src/main/java/org/broadinstitute/hellbender/tools/copynumber/GermlineCNVCaller.java @@ -108,12 +108,12 @@ * 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.

* - *

Note that {@link GermlineCNVCaller} can be run on larger interval sets by scattering them into smaller “shards.” + *

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.

* *

By default, {@link GermlineCNVCaller} will attempt to use all CPU cores accessible to it within the runtime - * environment. Two environment variables — MKL_NUM_THREADS and OMP_NUM_THREADS — control the + * environment. Two environment variables - MKL_NUM_THREADS and OMP_NUM_THREADS - control the * parallelism of the underlying linear algebra libraries.

* *

Runtime is also affected by how fast the inference procedure converges. There are multiple tool arguments that can