Jul 25, 2018

Whole-Genome Shotgun Sequence CNV Detection Using Read Depth

Methods in Molecular Biology
Fatma Kahveci, Can Alkan

Abstract

With the developments in high-throughput sequencing (HTS) technologies, researchers have gained a powerful tool to identify structural variants (SVs) in genomes with substantially less cost than before. SVs can be broadly classified into two main categories: balanced rearrangements and copy number variations (CNVs). Many algorithms have been developed to characterize CNVs using HTS data, with focus on different types and size range of variants using different read signatures. Read depth (RD) based tools are more common in characterizing large (>10 kb) CNVs since RD strategy does not rely on the fragment size and read length, which are limiting factors in read pair and split read analysis. Here we provide a guideline for a user friendly tool for detecting large segmental duplications and deletions that can also predict integer copy numbers for duplicated genes.

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Mentioned in this Paper

Genome-Wide Association Study
Size
Gene Dosage
Whole-Genome Shotgun Sequencing
Genome
Genes
Segmental Duplications, Genomic
Synaptic Vesicles
Research Personnel
Gene Deletion

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