期刊
BIOINFORMATICS
卷 28, 期 10, 页码 1307-1313出版社
OXFORD UNIV PRESS
DOI: 10.1093/bioinformatics/bts146
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资金
- Peter MacCallum Cancer Foundation
- Victorian Breast Cancer Research Consortium
- Australian Research Council [DP1096296]
- Australian Research Council [DP1096296] Funding Source: Australian Research Council
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.
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