vannotator

Introduction

This program annotates a VCF file using VEP. Given a VCF file, a CSV is generated containing the following fields:

1. chrom: The chromosome containing the variant.
2. pos: The position within the chromosome containing of the variant.
3. ref: The reference sequence of the variant.
4. alt: The alternate sequence of the variant.
5. depth: The depth, or total coverage of the region in scope.
6. allele_depth: The depth of the allele.
7. ratio_perc: The percentage of the reads that map to the variant vs those that map to the reference.
8. var_type: The type of the variant, i.e. SNP, insertion, deletion, CNV, etc.
9. effect: The coding effect of the variant, i.e. protein coding, intron variant, etc.
10. minor_allele_freq: The minor allele frequency, if present.

Installation

This software was implemented to support both Anaconda and Poetry paradigms.

Brief Synopsis

Using a single HTTPS session for RESTful API calls, multiple requests are sent to annotate each variant in a VCF file