Code for "Quantifying negative selection on synonymous variants" (HGG Advances, 2024)

The "Data" pipeline

data/ contains Hail and Snakemake code that requires execution in Google Cloud and saves files to a Google Storage bucket. Copies of the generated files are available in files/.

How to run

1. Create a new cluster: hailctl dataproc start <cluster_name> --packages snakemake==6.6.1 --requester-pays-allow-buckets gnomad-public-requester-pays --project <project_name> --bucket <bucket_name> --region <region> --num-workers <N> --image-version=2.0.27-debian10
   • as of this writing, the command runs gcloud dataproc clusters create and installs the following packages: --metadata=^|||^WHEEL=gs://hail-common/hailctl/dataproc/0.2.74/hail-0.2.74-py3-none-any.whl|||PKGS=aiohttp==3.7.4|aiohttp_session>=2.7,<2.8|asyncinit>=0.2.4,<0.3|bokeh>1.3,<2.0|boto3>=1.17,<2.0|botocore>=1.20,<2.0|decorator<5|Deprecated>=1.2.10,<1.3|dill>=0.3.1.1,<0.4|gcsfs==0.8.0|fsspec==0.9.0|humanize==1.0.0|hurry.filesize==0.9|janus>=0.6,<0.7|nest_asyncio|numpy<2|pandas>=1.1.0,<1.1.5|parsimonious<0.9|PyJWT|python-json-logger==0.1.11|requests==2.25.1|scipy>1.2,<1.7|tabulate==0.8.3|tqdm==4.42.1|google-cloud-storage==1.25.*
   • access to some annotation tables may also require adding --requester-pays-allow-annotation-db
2. Connect to the cluster: gcloud beta compute ssh <user_name>@<cluster_name>-m --zone "<zone>" --project "<project_name>"
3. git clone this repository and navigate to data/
4. Run the pipeline: snakemake --cores all --configfile config.yaml --config gcp_rootdir="<bucket_name>/some_directory/" gcp_username="<user_name>"

The pipeline uses pre-calculated SpliceAI scores from Jaganathan et al. Cell 2019. Please, copy exome_spliceai_scores.vcf.gz from https://basespace.illumina.com/s/5u6ThOblecrh (supplementary data) to your preferred GS bucket and provide a path to it as an additional --config argument for Snakemake: spliceai_scores_path="gs://<bucket_name>/some_directory/exome_spliceai_scores.vcf.gz".

The "Analysis" pipeline

analysis/ contains scripts that reproduce the figures from the main paper and the supplement using files created in data/.

How to run

snakemake --cores all --config gcp_rootdir="<bucket_name>/some_directory/" gcp_username="<user_name>"