SICtools

SICtools identifies single nucleotide variants (SNVs) and indels between two closely related BAM files by performing pairwise base-level comparisons across specified genomic regions to quantify and test allele-count differences.

Key Features:

• Pairwise Comparison: Performs base-level comparison between two BAM files across specified genomic regions to detect SNVs and indels.
• Statistical Analysis: Applies Fisher's exact test to base counts for statistical inference of allele-frequency differences.
• Euclidean Distance Calculation: Computes Euclidean distances from base counts (A, T, G, C) to provide a quantitative measure of divergence at each position.
• Indel Read Count Analysis: Accounts for indels using read counts and considers indels that span no less than two base pairs on both sides of the indel region.

Scientific Applications:

• Comparative Genomics: Detects fine-scale SNV and indel differences between related samples for comparative genomics studies.
• Evolutionary Biology: Enables detection of sequence variation relevant to evolutionary and population genetic analyses.
• Genetic Diversity Analysis: Supports assessment of genetic diversity and intra-sample heterogeneity by quantifying allele-level differences.
• Phenotype and Disease Association: Identifies candidate SNVs and indels that may contribute to phenotypic variation or disease susceptibility.

Methodology:

Performs pairwise comparison analyzing each base position across specified genomic regions and uses Fisher's exact test and Euclidean distance on base counts (A, T, G, C) and indel read counts, with indels considered when reads span no less than two base pairs on both sides of the indel region.