Diagnostic-style WES analysis of CVID/IEI-associated genes in public SRA samples using Galaxy

This dataset contains an English-language GitHub/Zenodo-ready package for a reproducible Galaxy-based diagnostic-style whole-exome sequencing analysis of public ENA/SRA samples SRR17215054 and SRR17215055. The analysis focuses on genes associated with common variable immunodeficiency (CVID) and inborn errors of immunity (IEI). The workflow includes quality control, trimming, alignment to GRCh38/hg38, BAM processing, variant calling with FreeBayes, annotation with SnpEff/SnpSift, CVID/IEI gene-panel filtering and comparison of candidate variants between samples. Input data:- BioProject / Study accession: PRJNA788443- Secondary study accession: SRP350501- BioSample: SAMN20448400- Secondary sample accession: SRS9614878- Experiments: SRX13394972 and SRX13394971- Runs: SRR17215054 and SRR17215055- Organism: Homo sapiens- Platform: Illumina HiSeq 2500- Library strategy: WXS- Library layout: single-end After filtering, 9 missense variants were retained in CVID/IEI-associated genes. The highest-priority candidate variants were NFKB1 c.691C>T p.R231C, PIK3CD c.3071G>A p.R1024H and TNFRSF13C c.62C>G p.P21R. This is an educational/research-style reanalysis of public sequencing data and is not a clinical diagnostic report. Variant interpretation requires independent validation, phenotype correlation, population frequency assessment, ClinVar/ClinGen review and formal ACMG/AMP classification.