Genomics Pipeline for Streamlined Variant Discovery and Annotation

Project Description

This document demonstrates a complete variant calling and annotation pipeline that starts with FastQ datasets. The pipeline utilizes open-source bioinformatic programs to process resulting reads, align them to the human genome (GRCh38), call genetic variants, and functionally annotate them.

The pipeline imitates a ClinGen workflow and includes all necessary steps—quality control, adapter trimming, alignment, variant calling, filtering, and annotation—using existing command line tools.

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Problem Statement

To perform quality control, alignment, variant calling, filtering, and annotation on sequencing data from SRR576933 using tools like FastQC, BWA, SAMtools, bcftools, and SnpEff.

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Workflow and Tools

• Data Source: Public FASTQ dataset (SRR576933) from SRA.
• Reference Genome: GRCh38 from GENCODE.
• Tools Used:
  • FastQC – Read quality control
  • Trimmomatic – Adapter and low-quality trimming
  • HISAT2 – Read alignment to reference genome
  • SAMtools – Format conversion and sorting
  • bcftools – Variant calling and filtering
  • SnpEff – Variant annotation

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Results

Output Files:

File Name	Description
SRR576933_trimmed.fastq	Trimmed high-quality reads
SRR576933_sorted.bam	Sorted alignment file
variants.vcf	Raw variants called
filtered_variants.vcf	Filtered variants (QUAL ≥ 20, DP ≥ 10)
annotated_filtered_variants.vcf	Functionally annotated variant set

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Repository Contents

• raw_data/: Original FASTQ file
• ref/: GRCh38 reference genome and index files
• trimmed/: Cleaned reads after Trimmomatic
• alignment/: BAM files, variant calls, and sorted data
• snpeff/: Annotated VCF output from SnpEff
• scripts/: Shell commands and helper scripts used

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How to Use

1. Clone the repository:

   git clone https://github.com/ParthivRajesh/Clinical-Genomics-VariantPipeline.git
   cd Clinical-Genomics-VariantPipeline