Bioinformatics Officer (Structural Variation)

Technology and Innovation

Hong Kong Science Park, Sha Tin / JC STEM Lab of Computational Genomics, CUHK

See All Job Openings

The Bioinformatics Officer (Structural Variation) operates and extends the structural variant (SV) calling pipeline that produces the Hong Kong and Lingnan population SV database from the Hong Kong Genome Project (HKGP) whole-genome sequencing data.  This is a project-based role where the incumbent will own the day-to-day production of jointly called SV callsets at scale, their benchmarking against public truth sets, their validation against long-read data, and subsequent population and clinical analyses.

Reporting to the Bioinformatics Consultant cum Principal Investigator of the Lingnan Population Structural Variant Database project, the incumbent will assume the following responsibilities:

Key Responsibilities

  • Operate and monitor per-sample SV discovery and cohort-wide joint genotyping at scale across HKGP short-read genomes, while managing batching, server scheduling, failure recovery, and step-by-step guides
  • Test pipeline accuracy against public SV truth sets; create per-class precision, recall, F1 and genotype-concordance reports for every pipeline change, and compile the release QC report
  • Validate short-read callsets against long-read sequencing data on HKGP genomes; track false-discovery rates per SV class to optimise filtering thresholds
  • Analyse and prepare the evidence packs for complex (CPX), multi-allelic copy-number (mCNV), and translocation (CTX) SV classes
  • Compute cohort allele frequencies and class-level statistics for the database releases, performing population-structure and admixture analyses of the local cohort against global reference panels
  • Contribute scientific methods, results and figures to the joint research project; presenting findings at project meetings and at project checkpoints
  • Perform any other duties assigned by senior officers

Requirements

We are seeking a high-calibre candidate for the post of Bioinformatics Officer (Structural Variation) who possesses:

  • A Master’s degree or above in bioinformatics, computational biology, computer science or a related discipline 
  • Experience in analysing human whole-genome sequencing data at cohort scale (hundreds to thousands of genomes)
  • Demonstrated hands-on experience with short-read structural variant discovery and joint genotyping, as well as SV benchmarking against GIAB or assembly-based truth sets using tools like Truvari
  • Working knowledge of long-read sequencing data (PacBio HiFi, Oxford Nanopore) and long-read SV callers (e.g. Sniffles2, pbsv, sawfish, cuteSV), sufficient to design an orthogonal validation
  • Strong command of Linux, shell scripting and Python; proficiency with htslib-family tools (samtools, bcftools), and formats like CRAM/VCF specifications
  • Statistical competence in population genetics (allele-frequency estimation, principal-component and admixture analysis, Mendelian consistency) and skills in reporting precision, recall and F1 with confidence intervals
  • Familiarity with public genomic resources and standards, such as: gnomAD, 1000 Genomes, HGSVC, dbVar, ClinVar, Ensembl/UCSC, GRCh38 and T2T-CHM13, and the GA4GH data standards (VCF 4.4+, VRS 2.x)
  • Understanding of research data governance for human genomic data, including de-identification, controlled-access environments and the Hong Kong Personal Data (Privacy) Ordinance
  • Clear written and spoken English; ability to present technical results to a mixed scientific, clinical and management audience. Cantonese or Mandarin is an advantage

Preferred Qualifications and Experience

  • A PhD degree in a relevant field
  • Experience with at least one workflow language (WDL with Cromwell, or Nextflow) and container runtimes (Docker, Singularity/Apptainer)
  • Disciplined software engineering practice: Git, code review, versioned configuration, unit tests for data-transforming code, and reproducible environments.  Responsible use of AI-assisted development tools while remaining accountable for all code and results produced
  • A strong publication record in genomics methods or population genomics
  • Prior contribution to open-source bioinformatics software

Office Location

Hong Kong Science Park, Sha Tin / JC STEM Lab of Computational Genomics, CUHK

Remuneration

Successful candidate will be offered attractive remuneration and be appointed on a one-year fixed-term contract.

Application

Interested parties should send full resume, enclosing current and expected remuneration together with availability, to HKGI by clicking "Apply Now" on or before 18 November 2026. Only shortlisted candidates will be notified.

Data collected will be used for recruitment purpose only.