bio-workflows-fastq-to-variants

What problem does it solve?

This workflow automates the end-to-end process of turning raw FASTQ reads into high-confidence variant calls, reducing manual integration work for sequencing analyses.

Core Features & Use Cases

• QC and preprocessing of FASTQ data with fastp
• Alignment of reads with bwa-mem2 and BAM generation
• BAM processing: sorting, deduplication, and indexing
• Variant calling with bcftools or GATK, including joint calling options
• Flexible use for whole-genome or exome projects, with optional BQSR

Quick Start

Provide paired-end FASTQ files and a reference genome, then run the workflow to generate a final VCF.