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Who needs geneyx anlysis API?

If you are Geneyx Analysis user that want to automate your data flow, for example:

  • Integrate your sequencing machine and automatically send FASTQ to Geneyx Analysis
  • Integrate with your LIMS and automatically create VCF samples or download reports
  • Integrate with your EMR and uploading clinical data to the patient record

The following items listed provide details for accomplishing these functions. If there is a feature that you would like to have, please contact support@geneyx.com.

Examples

Uploading sample to Geneyx Analysis

For automating the process of uploading VCFs to Geneyx Analysis you can use the two files scripts/ga.config.yml - request api key and user key from Geneyx Support edit the file and enter to the right places scripts/ga_uploadSamples.py - A python script that does the upload processing together with sample and patient data. please run it and check the command line arguments. You can read more at docs/geneyx.analysis.api.pdf scripts/ga_uploadSamplesWin.py - The windows version of previous script since some component changed on windows

Unifying Dragen SV/CNV/Repeat files

Illumina's Dragen pipeline creates by default 4 types of VCF files

  • SNVs
  • SV/CNV/Repeat for uploading those files to Geneyx Analysis it is required to merge the SV/CNV/Repeat files and upload the merged file as unified SV. For doing so one can use scripts/UnifiedVcf.py The script takes as parameters the three VCF files created by DRAGEN SV/CNV/Repeats and creates a unified SV file.

Running prerequisites:

  1. Python 3.9.
  2. bgzip

Windows Installation

On windows it is required to install python and also related components for using the ga_uploadSamplesWin.py

  1. Install Python
  2. From Admin command line
  • python -m pip install --upgrade pip
  • pip install PyYAML
  • pip install requests