Introduction

MOTIVATION: In light of the increasing adoption of targeted resequencing (TR) as a cost-effective strategy to identify disease-causing variants, a robust method for copy number variation (CNV) analysis is needed to maximize the value of this promising technology. RESULTS: We present a method for CNV detection for TR data, including whole-exome capture data. Our method calls copy number gains and losses for each target region based on normalized depth of coverage. Our key strategies include the use of base-level log-ratios to remove GC-content bias, correction for an imbalanced library size effect on log-ratios, and the estimation of log-ratio variations via binning and interpolation. Our methods are made available via CONTRA (COpy Number Targeted Resequencing Analysis), a software package that takes standard alignment formats (BAM/SAM) and outputs in variant call format (VCF4.0), for easy integration with other next-generation sequencing analysis packages. We assessed our methods using samples from seven different target enrichment assays, and evaluated our results using simulated data and real germline data with known CNV genotypes.

Publications

  1. CONTRA: copy number analysis for targeted resequencing.
    Cite this
    Li J, Lupat R, Amarasinghe KC, Thompson ER, Doyle MA, Ryland GL, Tothill RW, Halgamuge SK, Campbell IG, Gorringe KL, 2012-05-01 - Bioinformatics (Oxford, England)

Credits

  1. Jason Li
    Developer

  2. Richard Lupat
    Developer

  3. Kaushalya C Amarasinghe
    Developer

  4. Ella R Thompson
    Developer

  5. Maria A Doyle
    Developer

  6. Georgina L Ryland
    Developer

  7. Richard W Tothill
    Developer

  8. Saman K Halgamuge
    Developer

  9. Ian G Campbell
    Developer

  10. Kylie L Gorringe
    Investigator

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Summary
AccessionBT006811
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesR
User InterfaceTerminal Command Line
Download Count0
Submitted ByKylie L Gorringe