Required Software¶

If you have any questions or issues, feel free to open an issue or directly email Drew Neavin (d.neavin @ garvan.org.au)

This table illustrates the input that the pipeline requires to run and whether it is provided or needs to be prepared and provided by the user.

Input	Example Included with Test Data?
Sample Table tsv	Yes
Cellranger output directory	Yes
Reference genotypes vcf	Yes
Per pool files that contain individual IDs	Yes

Singularity Image¶

You will also need the Singularity image (has all softwares needed for the pipeline installed for consistency across different systems). Most HPCs have Singularity installed so you should be able to run Singularity images without any issue. If you are unsure, try running singularity –help. If Singularity is not installed on your HPC, reach out to your system administrators and see if they can install it. Otherwise, feel reach out to us and we can find another solution.

Download the singularity image (~6Gb) with the following command:
```
wget https://www.dropbox.com/s/ib78j88g5my15fs/WG1-pipeline-QC_imputation.sif
wget https://www.dropbox.com/s/he89x6xg915b4c3/WG1-pipeline-QC_imputation.sif.md5
```
Again, please make sure that the image is uncorrupted by comparing the md5sum
```
md5sum WG1-pipeline-QC_imputation.sif > downloaded_WG1-pipeline-QC_imputation.sif.md5
diff -s WG1-pipeline-QC_imputation.sif.md5 downloaded_WG1-pipeline-QC_imputation.sif.md5
```
Note

With the implementation of newer versions of the pipeline, it is important to make sure your singularity image alignes with the version of the pipeline documentation that you are currently using. To check the version of your singluation image plase run:
```
singularity inspect WG1-pipeline-QC_imputation.sif
```
which will tell you the image version you are currenlty using and, therefore, the relevant documentation for that image.
Next, please set up the pipeline with the following command; you will need to provide an absolute directory path to allow singularity to find the correct directories - this must be a directory somewhere above where you current working directory or the current working directory itself:
```
singularity run --bind <absolute_directory_path> --app setup WG1-pipeline-QC_imputation.sif .
```
Note

The pipeline expects certain files pulled from the image to be in the same directory as the singularity image so you will have to rerun the setup steps if you move the image

Optional¶

If you want to test the pipeline on your system you can use the test dataset we have provided in the image, run the following to get the test dataset from the image to your local directory:

singularity run --bind <absolute_directory_path> --app test_dataset WG1-pipeline-QC_imputation.sif .
tar -xzf ImputationTestDataset_plink.tar.gz

Install Snakemake¶

You will also need Snakemake and scipy to run the pipeline. We highly recommend you use th conda environment that we have prepared with all the requirements. The conda environment yaml (snakemake.yaml) should have been copied into your local directory when you set up the singularity image above.

To make a conda environment from this yaml, you can run:

conda env create -f snakemake.yaml -n wg1_snakemake

Then, to activate this environment, run:

conda activate wg1_snakemake

If you would prefer to install snakemake and scipy yourself, you can follow the instructions for installing Snakemake and then install scipy with pip install scipy.

Next Steps¶

Now that you have all the required files organized and the software installed, you can move on to running the SNP genotype imputation pipeline.