Results from WGS

After running the WGS analysis pipeline, a set of structured output folders is generated. These outputs include raw data processing, variant calling, annotation, and summary reports, all essential for downstream interpretation and reproducibility.

This section outlines the purpose of each output folder and what you should expect to find inside. Below is the file structure of the results folder -

results/
├── annotation/
├── csv/
├── multiqc/
├── pipeline_info/
├── preprocessing/
├── reference/
├── reports/
└── variant_calling/

The table below describes the contents of each folder -

Folder with outputs

Folder	Contents	Description
preprocessing/	FASTQ, BAM, trimming reports	Contains cleaned, aligned, and sorted reads. May include outputs from tools like BWA, SAMtools, GATK MarkDuplicates (e.g., duplicate marking).
variant_calling/	.vcf, .bcf, .g.vcf	Raw and filtered variant call files from GATK or other callers. May include SNPs, INDELs, and structural variants.
annotation/	.vcf, .txt, .csv	Functionally annotated variants (e.g., via VEP, SnpEff), including gene impacts, allele frequencies, and clinical significance.
csv/	Summarized tables	Processed or summarized tabular results, often for downstream stats, visualization, or integration.
multiqc/	multiqc_report.html	Unified quality control report covering FastQC, alignment stats, duplicate rates, coverage, etc.
pipeline_info/	.yaml, .txt, .log	Workflow configuration, software versions, and run metadata for reproducibility.
reference/	Reference genome, index files	FASTA and prebuilt index files (e.g., BWA, GATK, VEP), used during alignment and variant calling.
reports/	PDF/HTML/Markdown summaries	High-level summaries including coverage reports, alignment metrics, variant stats, or project-level documentation.

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Key output files

Checklist

File type	Description
*.bam, *.bai	Aligned reads and index files (for IGV or variant callers)
*.vcf, *.bcf	Variant calls, raw and filtered
annotated.vcf	Variants with gene annotations and clinical tags
coverage.txt, stats.csv	Coverage summaries per chromosome or sample
multiqc_report.html	Visual dashboard for QC metrics

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Output Validation Checklist

Checklist

Step	Validation
Read quality (FastQC)	Mean Q > 30, even distribution
Alignment (BAM files)	>95% mapped reads, proper pairing
Duplicate removal	Duplicates marked or removed
Variant calling success	Reasonable number of SNPs/INDELs
Variant annotation	Annotated VCFs with gene and effect info
QC overview	All tools successfully summarized in MultiQC

To explore more in-depth explanations for interpreting your FASTQC and multiQC reports, you can use this video link for multiQC and this manual for FASTQC.