Variant Annotation and prioritization

Question

[mandar.bedse]

I have data of Whole Exome Data of Human with Pancreatic Cancer patient: I would like you to, 1. Annotate the variants 2. Prioritize variants on various parameters of importance
3. Extract Genotype information for the Non-Synonymous Variants.

Could anybody suggest me the tools to achieve this objective?

Answer 1

[Vitis]

The annotation tools snpEff would be a good start. You may also look at PyVCF to extract genotypes from VCF files.

http://snpeff.sourceforge.net

https://pyvcf.readthedocs.io/en/latest/