Germline VCF Annotator: a lightweight pipeline for processing germline VCFs with robust variant extraction and read...

Area of Science:

• Genomics
• Bioinformatics
• Cancer Research

Background:

• Variant Call Format (VCF) files are difficult for direct human review and can be distorted by spreadsheet software.
• Annotating variants with gene context and functional consequences is crucial for understanding their impact.
• Existing annotation tools may not provide standardized, human-readable summaries with retained allele provenance.

Purpose of the Study:

• To develop a method for normalizing and annotating germline VCFs for easier human review and analysis.
• To investigate the role of DNA damage response (DDR) gene variations in mutation patterns within normal colon crypts.
• To assess potential associations between DDR variations, age, and treatment exposure in colon crypts.

Main Methods:

• Adapted Ensembl VEP to create standardized consequence fields across genomic features.
• Developed a two-step workflow: Germline VCF normalization and VEP annotation.
• Extracted variants of interest, appended read-evidence metrics, and assigned QC classes.

Main Results:

• Near-perfect concordance was achieved across technical repeats for predefined DDR loci after filtering.
• Discordance was primarily concentrated among Low-QC loci.
• No age-related trend in DDR burden was observed in bulk or crypt-derived samples.

Conclusions:

• The Germline VCF Annotator provides a reproducible, table-based format for analyzing variants.
• The tool facilitates human-readable locus-level summaries with retained allele provenance and read evidence.
• The developed workflow is applicable to other gene sets beyond DDR for variant analysis.