RSID Extraction Tool

These Python scripts extracts RSIDs (Reference SNP IDs) for genomic variants using the Ensembl REST API (assuming HG38). It retrieves RSIDs based on chromosome and position, and writes the results to an output CSV file.

VCF Annotation Extraction

These scripts extracts the relevant column of a VCF annotated with SNPeff (https://pcingola.github.io/SnpEff/snpeff/introduction/) and seperates "gene ID" and associated consequences.

Features

• Retrieves RSIDs from the Ensembl REST API using GFF3-formatted responses.
• Handles chromosome and position data efficiently, the script currently removes "chr" from the variant_id column.

Requirements

To install these dependencies, run:

pip install pandas requests pyreadr