Advances in next generation sequencing (NGS) technologies, in the past half decade, have enabled many novel genomic applications and have generated unprecedented amounts of new knowledge that is quickly changing how biomedical research is being conducted, as well as, how we view human diseases and diversity. As the methods, algorithms and software used to process NGS data are constantly being developed and improved, performing analysis and determining the validity of the results become complex. Moreover, as sequencing moves from being a research tool into a clinical diagnostic tool understanding the performance and limitations of bioinformatics pipelines and the results they produce becomes imperative. This thesis aims to assess the performance of nine bioinformatics pipelines for sequence read alignment, variant calling and genotyping in a Mendelian inherited disease, parent-trio exome sequencing design. A well-characterized reference variant call set from the National Institute of Standards and Technology and the Genome in a Bottle Consortium is be used for producing and comparing the analytical performance of each pipeline on the GRCh37 and GRCh38 human references.

Library of Congress Subject Headings

Exomes; Genomics; Algorithms--Evaluation

Publication Date


Document Type


Student Type


Degree Name

Bioinformatics (MS)

Department, Program, or Center

Thomas H. Gosnell School of Life Sciences (COS)


Michael V. Osier

Advisor/Committee Member

John M. Ashton

Advisor/Committee Member

Steven R. Gill


Physical copy available from RIT's Wallace Library at QH447 .C67 2015


RIT – Main Campus

Plan Codes