verifyBamID

verifyBamID detects within-species DNA sample contamination and sample swaps by estimating contamination levels from sequencing reads and array-based genotype data to assess impacts on genotype accuracy.

Key Features:

• Contamination Detection: Identifies contamination using three modes: combined sequencing reads and array-based genotypes, sequencing reads alone, and array-based genotypes alone.
• Pre- and Post-Sequencing Analysis: Performs contamination analysis both after sequence data generation (prior to variant calling) and before sequencing using array-based genotypes.
• Robust Contamination Estimation: Validated with in silico and experimentally contaminated samples and capable of detecting and estimating contamination levels as low as 1%.
• Sample Swap Detection: Detects sample swaps by comparing sequencing reads to previously known genotypes for an individual or group of individuals.
• Contamination Impact Evaluation: Assesses the effect of DNA contamination on genotype accuracy and screens for contamination-related genotype misclassification.

Scientific Applications:

• High-precision genomic studies: Quality-controls genotype calls in studies requiring high precision in genotype classification.
• Large-scale sequencing projects: Detects and quantifies cross-sample contamination that could skew results in large cohorts.
• Rare variant studies: Identifies contamination risks in analyses of rare genetic variants where minimal contamination can alter outcomes.

Methodology:

Leverages a dual-method strategy using sequencing reads and array-based genotypes to detect contamination, estimate contamination levels, and identify sample swaps.