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Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Targeted Next-generation Sequencing and Bioinformatics Pipeline to Evaluate Genetic Determinants of Constitutional Disease

Published on: April 4, 2018

Improving bioinformatic pipelines for exome variant calling.

¹Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA. genomics_ji@stanford.edu.

Genome Medicine

|February 1, 2012

Summary

This summary is machine-generated.

Atlas2 is a new, accessible variant calling tool for exome sequencing data. It provides a rapid and cost-effective solution for identifying genetic variants, even for researchers without extensive bioinformatics resources.

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Area of Science:

Genomics
Bioinformatics
Computational Biology

Background:

Exome sequencing is cost-effective for identifying coding region variants.
Identifying single nucleotide variants, insertions, and deletions is challenging.
Many researchers and labs lack necessary bioinformatics pipelines for clinical exome analysis.

Purpose of the Study:

To introduce the Atlas2 suite as an accessible variant calling solution.
To evaluate Atlas2's performance compared to existing variant callers.
To provide a rapid data processing alternative for exome sequencing.

Main Methods:

Exome sequencing data analysis.
Variant calling using the Atlas2 suite.
Comparison of Atlas2 with other popular variant callers on desktop and cluster environments.

Main Results:

Atlas2 performs comparably to other popular variant callers.
The Atlas2 suite is designed for wide accessibility and scalability.
Atlas2 can run on desktop computers and computational clusters.

Conclusions:

Atlas2 offers an accessible alternative for exome sequencing data processing.
It provides a rapid solution for variant calling, suitable for clinical applications.
Atlas2 democratizes variant identification for researchers and diagnostic labs.