Genomics Research Data Analyst II (Hybrid)

University of California San Diego; San Diego (CA); On-site; USD 50,000 - 69,000; Full time

Job summary

UC San Diego Pediatric researchers seek a Research Data Analyst 2 to build and optimize computational pipelines for sequencing and genotyping in HPC and cloud environments. You will implement workflows using Bash, PLINK, GATK, HipSTR and BEAGLE, ensuring quality control and thorough documentation.

The role emphasizes collaboration, data security, and the ability to communicate complex analyses. A strong background in bioinformatics and genome-wide analysis is essential, with experience in

Qualifications

• Six (6) years of related experience, education/training, OR a Bachelor’s degree in related area plus two years of related experience/training.
• Working knowledge of research function.
• Working skills in statistical analysis, systems programming, database design and data security measures.
• Working skills in analysis and consultation.
• Knowledge of bioinformatics software related to sequencing and genotyping, ability to stay abreast of the recent developments in the field.
• Proven ability to plan and conduct studies related to genotyping and genotyping quality control, optimize parameters in the bioinformatics computational pipelines.
• Knowledge of Linux-based workflow development, including Bash scripting.
• Extensive experience in developing multistep analysis pipelines/workflows using scripting languages including WDL.
• Demonstrated experience in handling big data sets, experience in programming languages, including R, Python.
• Knowledge of Linux, High Performance Computing, cloud technologies such as Amazon EC2, and the All of Us Research workbench.
• Proven ability to effectively manage time and see assigned parts of projects through to completion on deadline.
• Excellent communication skills.
• Working knowledge of sequencing and genotyping‑related software such as Bcftools, Bedtools, FastQC, Plink, Vcftools.
• Proven ability to carefully document the work and annotate the code. Experience in using software revision control systems (e.g. GIT).
• Experience performing genome-wide analysis of tandem repeat variation in human populations.

Responsibilities

• Under supervision, builds computational pipelines to perform sequence analysis and genotyping of humans and model organisms in HPC and cloud environments.
• Pipelines based on established workflows using Bash scripting and software such as PLINK, GATK, HipSTR, BEAGLE; perform routine quality control for data inputs and analysis outputs.
• Develops new pipelines under supervision, selecting software and testing different computational approaches.
• Documents work and annotates code with clear explanations; communicates findings effectively.
• Works on research data reporting assignments of moderate scope and diversity, following defined practices and policies.

Skills

Genotyping

Bioinformatics

Linux

Bash

Python

R

GIT

HPC

Cloud computing

Education

Bachelor’s degree in related field

Tools

GATK

PLINK

HipSTR

BEAGLE

Job description

UC San Diego Pediatric researchers seek a Research Data Analyst 2 to build and optimize computational pipelines for sequencing and genotyping in HPC and cloud environments. You will implement workflows using Bash, PLINK, GATK, HipSTR and BEAGLE, ensuring quality control and thorough documentation.

The role emphasizes collaboration, data security, and the ability to communicate complex analyses. A strong background in bioinformatics and genome-wide analysis is essential, with experience in