BAMixChecker

BAMixChecker detects sample mislabeling and verifies sample identity in next-generation sequencing (NGS) cohorts by assessing genotype concordance.

Key Features:

• Automated detection: Compares genotypes across a BAM file cohort to identify mismatched, orphan, or swapped samples automatically.
• High accuracy: Reports approximately 100% accuracy in identifying orphan and swapped samples across whole-exome sequencing (WES), RNA-Seq, and targeted sequencing panels of fewer than 50 genes.
• Flexible SNP analysis: Uses dataset-specific sets of single-nucleotide polymorphisms (SNPs) to compute genotype concordance tailored to the input data.
• Entropy-based file name analysis: Integrates entropy-based analysis of file names to assist detection of potential mismatches.
• Comprehensive reporting: Produces an HTML-style report with tables and heatmaps that visualize sample matching status and detected mismatch events.

Scientific Applications:

• Cohort-level sample integrity quality control: Detects and flags orphan and swapped samples within NGS cohorts to maintain dataset integrity.
• Whole-exome sequencing (WES): Assesses genotype concordance to verify sample identities in WES datasets.
• RNA-Seq: Evaluates genotype concordance for RNA-Seq samples to identify mislabeling or swaps.
• Targeted sequencing panels (<50 genes): Performs sample identity checks on small targeted panels using a reduced SNP set.

Methodology:

BAMixChecker computes genotype-concordance scores from dataset-specific SNP sets and integrates entropy-based file-name analysis to detect orphan and swapped samples.