Contra

Contra detects copy number variations (CNVs) from targeted resequencing data, including whole-exome capture, to identify copy number gains and losses relevant for genetic studies of disease.

Key Features:

• CNV detection: Identifies copy number gains and losses across target regions by analyzing normalized depth of coverage from sequencing data.
• GC-content bias removal: Mitigates GC-content bias using base-level log-ratios.
• Library size effect correction: Corrects for imbalances in library size that affect log-ratio calculations.
• Log-ratio estimation: Estimates log-ratio variations through binning and interpolation to smooth noise and refine copy-number estimates.
• File format integration: Accepts BAM/SAM alignments and outputs CNV calls in VCF 4.0.
• Targeted resequencing support: Operates on targeted resequencing datasets, including whole-exome capture and other target enrichment assays.

Scientific Applications:

• CNV discovery in targeted studies: Detects CNVs from targeted resequencing and whole-exome capture datasets for studies of genetic variation.
• Disease-associated variant analysis: Supports identification of genetic variations linked to disease by reporting copy number gains and losses.
• Benchmarking and validation: Has been evaluated using samples from seven target enrichment assays, simulations, and real germline data with known CNV genotypes.

Methodology:

Analyzes normalized depth of coverage from BAM/SAM, computes base-level log-ratios, applies GC-content and library-size corrections, performs binning and interpolation for log-ratio estimation, and outputs CNV calls in VCF 4.0.