or, if you forgot the `--recurse-submodules` option, run `git submodule update --init` after the cloning.
### 2.1 Install VEP
Clone VEP from the [official github](https://github.com/Ensembl/ensembl-vep). Installation details are provided there. As specified, run
Go to the ensembl-vep/ folder in tools/ and run
```
git clone https://github.com/Ensembl/ensembl-vep
cd ensembl-vep
perl INSTALL.pl
```
...
...
@@ -99,7 +105,7 @@ You may replace `/usr/local/bin` with whatever path where you usually save binar
### 2.3 Example
The main function for annotating a vcf is `run_annotator` in `main` module. Have a look at `run_example_tcga_GA.py` to have an example of how to run the tool and at the `run_annotator` documentation for more details about the options.
The main function for annotating a vcf is `run_annotator` in `main` module. Have a look at `run_example_tcga_GA.py` or `run_example_tcga_HS` to have examples of how to run the tool and at the `run_annotator` documentation for more details about the options.