inGAP-family

inGAP-family detects and filters artificial variants to improve identification of DNA polymorphisms, structural variants (SVs), meiotic recombination loci, and causal mutations from short-read alignments.

Key Features:

• Short-read alignment-based discovery: Discovers DNA polymorphisms and structural variants (SVs) through the alignment of short reads.
• Artificial-variant filtering: Filters out artificial variants arising from genome complexities and large-scale structural variations that can confound analyses.
• Non-allelic locus discrimination: Removes misinterpreted sequence differences between non-allelic loci to reduce false genotyping and incorrect estimation of allele frequencies.
• Recombination and mutation localization: Facilitates precise identification of meiotic recombination points and causal mutations within mutant genomes and quantitative trait loci (QTL).
• Evaluation of predicted variants: Enables further evaluation of predicted variants and identification of mutations related to specific genotypes.
• Real-dataset validation: Demonstrated applicability on real datasets for high-confidence polymorphism and SV analysis.

Scientific Applications:

• Meiotic recombination mapping: Mapping meiotic recombination loci with reduced confounding from structural variation-induced artifacts.
• Causal mutation identification: Detecting causal mutations in mutant genomes for mutant analysis and positional cloning.
• QTL and marker-assisted genetics: Supporting molecular marker-assisted genetic studies and QTL analysis by providing accurate polymorphism calls.
• Accurate genotyping and allele-frequency estimation: Improving genotyping accuracy and allele frequency estimates by removing artificial variants.
• Structural-variation-aware variant analysis: Analyzing the impact of large-scale structural variations on polymorphism detection in empirical datasets.

Methodology:

Discover DNA polymorphisms and structural variants (SVs) through alignment of short reads and filtering out artificial variants caused by genome complexities and large-scale structural variations.