Computational Cancer Researcher

A simple program counting SNPs and small indels

Dependencies

You need Python 3 since this program uses vcfpy which is only available in Python 3.

pip3 install vcfpy
pip3 install pysam

How to use

Simply call the main.py using python module on your machine (mine is python3) and it will run on the sample .VCF file (project.NIST.hc.snps.indels.vcf)

python3 main.py

How did I approach the problem?

1. What is .VCF file? - Variant Call Format
2. How can I open .VCF file programmatically? – I found a library written in Python called vcfpy which does exactly what I need vcfpy
3. What information does .VCF contain? I found a good documentation explain in details every aspect of .vcf file and what’s the meaning of each keyword in the file VCF v4.2 Specs
4. After hours of reading the specifications of .VCF file, I finally came to realize that there’s a simple way that can help me count: a. SNP: When there is a single base substitutions and there are only two alleles. (can be done using simple if statements) b. Indels: Total number of insertions and deletions (special case is when a record belongs to mix type, containing both insertion and deletion). (this can easily be solved by going through all alternate bases (if there are more than two)) c. Insertions: The reference base is replace with the reference base plus extra bases. (can be easily calculated using len() function) d. Deletions: The reference base is replace with the reference base plus extra bases. (can be easily calculated using len() function)
5. Read documentations and codebase of the library vcf GitHub and I came up with a simple counting program which is available in this GitHub link: https://github.com/quanglddev/Computational-Cancer-Researcher

This is used as an application for employment (Computational Cancer Researcher role at Drexel and Fox Chase Cancer Center.)