Genomics Data Analyst — Pipelines in HPC

UC San Diego; San Diego (CA); On-site; USD 95,000 - 130,000; Full time

Job summary

UC San Diego's Department of Pediatrics seeks a researcher to build and optimize computational pipelines for sequencing and genotyping in HPC and cloud environments. You will work with PLINK, GATK, HipSTR, BEAGLE, and related tools, ensuring data quality and reproducibility while documenting code and results.

You will collaborate across teams, manage multiple analysis projects, and communicate findings clearly in writing and speech.

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.
• Skills to communicate complex information in a clear and concise manner both verbally and in writing.
• 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, uses skills and knowledge of professional concepts in research data analysis.
• The main responsibility is building computational pipelines to perform sequence analysis and genotyping of humans and model organisms in HPC and cloud compute environments.
• This includes pipelines based on the established computational workflow, using Bash scripting and software such as PLINK, GATK, HipSTR, and BEAGLE; performing routine quality control for data inputs and analysis outputs, assisting with data organization and backup.
• Additional responsibility will include developing new pipelines, which require, under supervision, selecting software and testing different computational approaches.
• The successful applicant will have exceptional written and verbal communication, will carefully document their work and annotate their code.
• Excellent organization skills are required in order to work as part of a team.

Skills

Bash scripting

Python

R

Linux

Bioinformatics

Data analysis

Education

Bachelor's degree in related area

Tools

PLINK

GATK

HipSTR

BEAGLE

Bedtools

Bcftools

Vcftools

GIT

Job description

UC San Diego's Department of Pediatrics seeks a researcher to build and optimize computational pipelines for sequencing and genotyping in HPC and cloud environments. You will work with PLINK, GATK, HipSTR, BEAGLE, and related tools, ensuring data quality and reproducibility while documenting code and results.

You will collaborate across teams, manage multiple analysis projects, and communicate findings clearly in writing and speech.