Installation

download and extract the zip folder

cd into the extracted directory and run,

for Linux shell,

python setup.py sdist bdist_wheel
pip install dist/*whl

for Windows command line,

python setup.py sdist bdist_wheel
for %i in (dist\*.whl) do pip install %i

Input

It takes vcf file as input

Usage

from VariantAnnotator import *

ParseObj = Parser("yourVCFfile.txt")
variants = ParseObj.parseInput()
ANNOTATE(variants, output="myOutputFile.xlsx")

Output

It pulls following annotations for each variant within the vcf file

Base Annotations

1. Gene name
2. Variant biotype
3. Regulatory significance: Checks if the variant is within the regu;atory regions of the gene
4. Regulatory feature id: ENSEMBL regulatory feature id
5. Amino acids: Reports associated amino acid mutation
6. Codons: Reports associated codon mutation

Database Ids

7. rsid: variant dbSNP database id
8. Uniprot id: Variant Uniprot database id
9. Cosmic id: Variant Cosmic database id
10. Clinvar id: Variant Clinvar database id
11. PharmGKB ID: Variant PharmGKB database id

Amino acid mutation scores

12. SIFT: SIFT scare for the amino acid mutation
13. Polyphen: Polyphen score for amino acid mutation

Mutation frequency

14. American: Frequency of the variant in American population
15. South Asian: Frequency of the variant in South Asian population
16. East Asian: Frequency of the variant in East Asian population
17. African: Frequency of the variant in African population
18. European: Frequency of the variant in African population
19. Pubmed: Pubmed id for the corresponding variant

Below is the example output excel sheet image

Things to do

1. Error handelling
2. Add protein structure-function annotations