DITTO-API

!!! For research purposes only !!!

Repo for querying DITTO predictions for variants using FastAPI.

Requirements

Following are required:

• git
• python3.7+
• Docker

Installing

1. Clone the repository - change in to directory of your choice and run:

git clone https://github.com/uab-cgds-worthey/DITTO-API.git

2. Navigate to the project directory

cd DITTO-API

3. Build the Docker image

docker build -t ditto-api .

4. Run the Docker container

docker run -p 8000:8000 --name ditto-api ditto-api

5. Use this link in your browser to retrieve DITTO scores

http://localhost:8000/docs and use this variant as example: 1-2406483-C-G

Expected result

DITTO will output deleterious score by Ensemble transcript. Below is the output for the above test variant. To verify the scores, please query the variant in the DITTO web app.

{
  "scores_by_transcript": {
    "ENST00000288774.7": {
      "gene": "PEX10",
      "consequence": "intron_variant,splice_site_variant",
      "chrom": "chr1",
      "pos": "2406483",
      "ref_base": "C",
      "alt_base": "G",
      "DITTO": "1.0"
    },
    "ENST00000447513.6": {
      "gene": "PEX10",
      "consequence": "intron_variant,splice_site_variant",
      "chrom": "chr1",
      "pos": "2406483",
      "ref_base": "C",
      "alt_base": "G",
      "DITTO": "1.0"
    },
    "ENST00000507596.5": {
      "gene": "PEX10",
      "consequence": "intron_variant,splice_site_variant",
      "chrom": "chr1",
      "pos": "2406483",
      "ref_base": "C",
      "alt_base": "G",
      "DITTO": "1.0"
    },
    "ENST00000510434.1": {
      "gene": "PEX10",
      "consequence": "2kb_downstream_variant,NMD_transcript_variant",
      "chrom": "chr1",
      "pos": "2406483",
      "ref_base": "C",
      "alt_base": "G",
      "DITTO": "1.0"
    },
    "ENST00000378513.7": {
      "gene": "RER1",
      "consequence": "2kb_downstream_variant",
      "chrom": "chr1",
      "pos": "2406483",
      "ref_base": "C",
      "alt_base": "G",
      "DITTO": "1.0"
    },
    "ENST00000605895.6": {
      "gene": "RER1",
      "consequence": "2kb_downstream_variant",
      "chrom": "chr1",
      "pos": "2406483",
      "ref_base": "C",
      "alt_base": "G",
      "DITTO": "1.0"
    }
  }
}

Contributing

We welcome contributions! See the docs for guidelines.

Contact information

For issues, please send an email with clear description to

Name	Email
Tarun Mamidi	tmamidi@uab.edu
Brandon Wilk	bwilk777@uab.edu