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 |
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Clone the Tempus_Challenge directory from Github
git clone [email protected]:MediciPrime/Tempus_Challenge.git
- Change your working directory to the Tempus_Challenge directory
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Next, there are two ways to ensure the script will function properly:
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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>
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The script will output table.txt in TSV form containing the VCF annotations