CONTRA: copy number analysis for targeted resequencing
By Jason Li, Richard Lupat, Kaushalya C. Amarasinghe, E. Thompson, Maria A. Doyle, G. Ryland, R. Tothill, Saman Kumara Halgamuge, Ian G. Campbell, Kylie L. Gorringe. Bioinform., 2012
344 citations recorded by the source corpus.
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. Availability and implementation: Source code and sample data are freely available under GNU license (GPLv3) at http://contra-cnv.sourceforge.net/ Contact: Jason.Li@petermac.org Supplementary information: Supplementary data are available at Bioinformatics online.
Subfields: Cancer Research, Genetics
View Paper: https://www.semanticscholar.org/paper/1b716a75b284a77dbc1938b9f3cc411663710af4
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Citations in the corpus
- CNVkit: Genome-Wide Copy Number Detection and Visualization from Targeted DNA Sequencing (2016, methodology): “Tools have been developed for copy number analysis of these datasets, as well, including CNVer [6], ExomeCNV [7], exomeCopy [8], CONTRA [9], CoNIFER [10], ExomeDepth [11], VarScan 2 [12], XHMM [13], ngCGH [14], EXCAVATOR [15], CANOES [16], PatternCNV [17], CODEX [18], and recent versions of…”
- A survey of tools for variant analysis of next-generation genome sequencing data (2013, methodology): “ExomeCNV identified 137 CNVs, whereas CONTRA was able to call 8940 CNVs using a P-value 0.05.”
- Integrative and comparative genomic analysis of HPV-positive and HPV-negative head and neck squamous cell carcinomas (2014, methodology): “Copy-number analysis was performed using sequencing data and the CONTRA algorithm (25).”
- Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives (2013, methodology): “net/ Python SAM/BAM Comparing base-level log-ratios calculated from read depth between case and control samples [77]”