VCF generation

Definition

It is a python-based script that can take in genomic HGVS nomenclature and creates a VCF in a format that can be parsed by StrandOmics.

Execution

1. Clone the repository with the command -

    git clone https://github.com/sayantansls/vcf-generator.git
   

2. Once the repository is cloned, enter the directory vcf-generator and run the script setup.sh

    ./setup.sh
   

This will ensure all the dependecy files (human genome reference data) are downloaded and placed in their appropriate location. You can download the files separately as well

• GrCh37 - http://hgdownload.cse.ucsc.edu/goldenpath/hg38/bigZips/hg38.2bit
• GrCh38 - http://hgdownload.cse.ucsc.edu/goldenpath/hg19/bigZips/hg19.2bit

3. To run and use the vcf-generator, run the script run.sh

    ./run.sh
   

Once the script is run, it will ask for input to select certain parameters:

• Genomic Build - Enter 'A' for GrCh37 OR 'B' for GrCh38 (this genomic build will be used for mapping in the VCF)
• Use Case - The script either consumes a TSV file with headers Gene name and genomic HGVS with the data or it can take a single gene and genomic HGVS and create a VCF file. (Enter '1' for file option OR '2' for single gene and genomic HGVS option).

For the input file and output vcf format, check the examples at - /vcf-generator/data/examples/

Limitations

The script only consumes genomic HGVS nomenclature, not cDNA or protein nomenclature.

The limitations are currently being worked on and will be resolved in future versions

Contact

Author - Sayantan Ghosh ([email protected])