SECNVs: A Simulator of Copy Number Variants and Whole-Exome Sequences From Reference Genomes

Frontiers in Genetics
Yue XingClaudio Casola

Abstract

Copy number variants are duplications and deletions of the genome that play an important role in phenotypic changes and human disease. Many software applications have been developed to detect copy number variants using either whole-genome sequencing or whole-exome sequencing data. However, there is poor agreement in the results from these applications. Simulated datasets containing copy number variants allow comprehensive comparisons of the operating characteristics of existing and novel copy number variant detection methods. Several software applications have been developed to simulate copy number variants and other structural variants in whole-genome sequencing data. However, none of the applications reliably simulate copy number variants in whole-exome sequencing data. We have developed and tested Simulator of Exome Copy Number Variants (SECNVs), a fast, robust and customizable software application for simulating copy number variants and whole-exome sequences from a reference genome. SECNVs is easy to install, implements a wide range of commands to customize simulations, can output multiple samples at once, and incorporates a pipeline to output rearranged genomes, short reads and BAM files in a single command. Variants gener...Continue Reading

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Datasets Mentioned

BETA
ERR3385637

Methods Mentioned

BETA
exome-sequencing
Exome Copy
PCR
genotyping

Software Mentioned

ExomeDepth
CNV
R
SECNVs Simulator of
Samtools
CANOES
Simulator of Exome SECNVs
fasta
GATK
CODEX

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