pibase

pibase validates single-nucleotide variants (SNVs) inferred from next-generation sequencing by analysing alignment-file evidence to distinguish true variants from sequencing artifacts and coverage gaps for applications including clinical diagnostics, comparative genomics, archaeogenetics, and forensics.

Key Features:

• SNV validation: Leverages alignment-file details to identify reproducible genotypes and distinguish true SNVs from sequencing artifacts and coverage gaps.
• High specificity: Demonstrated 99.98% specificity in test cases, outperforming other available tools by roughly tenfold.
• Genomic scope: Applicable to diploid and haploid genomes, exome sequencing, and targeted enrichment datasets.
• Pair-wise nucleotide-signal comparisons: Performs pair-wise comparisons between samples using nucleotide signals to increase accuracy approximately tenfold over genotype-based approaches and to detect allelic imbalances in heterozygous SNVs.
• Detection in complex contexts: Detects SNVs within copy number variation loci and heterogeneous tumor sequences and accounts for coverage gaps that can cause missed or false variant calls.

Scientific Applications:

• Clinical diagnostics: Validation of SNVs used in diagnostic settings where distinguishing true variants from artifacts is critical.
• Comparative cell analyses: Comparison of healthy and affected cells, including monozygotic twin studies, to detect somatic differences and allelic imbalance.
• Archaeogenetics and forensics: Identification of true variants in contexts requiring high precision such as archaeogenetic dating and forensic analyses.

Methodology:

Analyses alignment-file evidence to identify reproducible genotypes and performs pair-wise nucleotide-signal comparisons between samples to validate SNVs and detect allelic imbalances.