This program can be used to convert whole genome sequence data stored in a BigQuery table with the Institute for Systems Biology. This covers over 1000 patient samples that have been processed against HG19 and are available for use for credentialed researchers.

To use this script, you first must set up your environment to support BigQuery through ISG. We recommend that you set up a virtual environment (not covered here).

The following software must be installed to support this script

• Google Cloud BigQuery Libraries: python -m pip install --upgrade google-cloud-bigquery

Your environment and access key can be set up following the directions at:

• https://cloud.google.com/bigquery/docs/quickstarts/quickstart-client-libraries#client-libraries-install-python

Usage information can be printed out by running the program with the help flag: python wgs_to_vcf.py --help

usage: wgs_to_vcf.py [-h] [--output_file OUTPUT_FILE] [--chromosome {chr19,chrX,chrY,chr6,chr18,chr14,chr7,chr12,chr17,chr2,chr9,chr1,chr5,chr10,chr20,chr22,chr8,chr15,chr3,chr16,chr13,chr21,chr11,chr4}] [--limit LIMIT] tcga_id

positional arguments:
  tcga_id               TCGA ID to generate a vcf file from.

optional arguments:
  -h, --help            show this help message and exit
  --output_file OUTPUT_FILE, -o OUTPUT_FILE
                        Set the output vcf file name.
  --chromosome {chr19,chrX,chrY,chr6,chr18,chr14,chr7,chr12,chr17,chr2,chr9,chr1,chr5,chr10,chr20,chr22,chr8,chr15,chr3,chr16,chr13,chr21,chr11,chr4}
                        Limit to a specific chromosome.
  --limit LIMIT, -l LIMIT
                        Limit the number of SNVs returned (for debugging primarily).

The required parameter is the TCGA ID of interest. For example:

python wgs_to_vcf.py TCGA-44-2656

You can also limit to a specific chromosome of interest. For example:

python wgs_to_vcf.py TCGA-44-2656 --chromosome chr4

The chromosomes which are allowed are listed in the help above. Chromosome format is in the 'chr#' syntax.

And finally, you can also limit the number of entries for testing or debugging purposes.

python wgs_to_vcf.py TCGA-44-2656 --chromosome chr4 --limit 20