Code review update.

README.md

@@ -72,25 +72,29 @@ releases of the toolkit.
 * Pre-packaged Docker images with all needed dependencies installed can be found on
   [our dockerhub repository](https://hub.docker.com/r/broadinstitute/gatk/). This requires a recent version of the
    docker client, which can be found on the [docker website](https://www.docker.com/get-docker).
-* Python Dependencies<a name="python"></a>
-    * GATK uses the [Conda](https://conda.io/docs/index.html) package manager to establish and manage the
-      environment and dependencies required by GATK tools that use Python There are two different conda environments
-      that can be used:
-        * The "gatk" environment, which has no special hardware requirements.
-        * The "gatk-intel" environment, which requires and uses Intel hardware acceleration to increase performance.
-        * The GATK Docker image comes with the "gatk" environment pre-configured.
-    * In order to establish the conda environment required to run these tools when not using the Docker image, do
-      the following:
-        * Make sure [Miniconda or Conda](https://conda.io/docs/index.html) is installed (Miniconda is sufficient).
-        * Create the environment:
-            * If running from a zip or tar distribution, just run the command ```conda env create -f gatkcondaenv.yml```.
+* Python Dependencies:<a name="python"></a>
+    * GATK4 uses the [Conda](https://conda.io/docs/index.html) package manager to establish and manage the
+      Python environment and dependencies required by GATK tools that have a Python dependency. There are two different
+      conda environments that can be used:
+        * The ```gatk``` environment, which has no special hardware requirements. The GATK Docker image comes with the
+          "gatk" environment pre-configured.
+        * The ```gatk-intel``` environment, which requires and uses Intel (AVX2 or AVX-512) hardware acceleration to
+          increase performance.
+    * To establish the conda environment when not using the Docker image, a conda environment must first be "created", and
+      then "activated":
+        * First, make sure [Miniconda or Conda](https://conda.io/docs/index.html) is installed (Miniconda is sufficient).
+        * To "create" the conda environment:
+            * If running from a zip or tar distribution, run the command ```conda env create -f gatkcondaenv.yml``` to
+              create the ```gatk``` environment, or the command ```conda env create -f gatkcondaenv.intel.yml``` to create
+              the ```gatk-intl``` environment.
             * If running from a cloned repository, run ```./gradlew localDevCondaEnv```. This generates the Python
               package archive and conda yml dependency file(s) in the build directory, and also creates (or updates)
-              a local conda environment named "gatk".
-        * Activate the environment:
-            * Once the environment has been created, it must be activated from within the shell from which GATK is
-              run whenever tools with a Python dependency are executed. To activate the environment, execute the
-              shell command ```source activate gatk```.
+              the local  ```gatk``` conda environment. (To create the ```gatk-intel``` conda environment once the files
+              have been generated, run the command ```conda env create -f gatkcondaenv.intel.yml```).
+        * To "activate" the conda environment (this must be done from within the shell from which GATK is run whenever
+          tools with a Python dependency are executed):
+             * Execute the shell command ```source activate gatk``` to activate the ```gatk``` environment, or
+               ```source activate gatk-intel``` to activate the ```gatk-intel``` environment.
         * See the [Conda](https://conda.io/docs/user-guide/tasks/manage-environments.html) documentation for
           additional information about using and managing Conda environments.