/Tempus_Challenge

Primary LanguagePython

VCF Parser

This script parses a VCF file and outputs a table in tab-separated values (TSV) form.
The table contains the following columns:

Key Description
Chr Chromosome variant is locationed on
Position Variants' location on the chromosome
Ref Reference Allele
Alt Alternate Allele
Annotation Type of variant e.g. snp, insertion, del
SeqDepth Total read depth at variant location
VSReads Total number of reads representing the variant i.e. Variant Supporting Reads
PVSReads Percent of reads representing the variant
AFrequency Allele Frequency according to ExAC Browser - Harvard
AGene Affected gene according to ExAC Browser - Harvard

Setup

  1. Clone the Tempus_Challenge directory from Github

    • git clone git@github.com:MediciPrime/Tempus_Challenge.git
    • Change your working directory to the Tempus_Challenge directory

  2. Next, there are two ways to ensure the script will function properly:

    • Install Miniconda
      • Once installed, setup Tempus environment w/ the following code:
      • conda env create -f environment.yml
      • Activate tempus environment
        • source activate tempus
    • Install python3 and install the requests package
      • pip install requests

  3. After performing either of the two steps above cd into the folder containing the script

    • Ensure that vcf_parser.py is executable
    • Run python vcf_parser.py <insert vcf file location>

  4. The script will output table.txt in TSV form containing the VCF annotations