Heap

Heap detects single nucleotide polymorphisms (SNPs) in low-coverage next-generation sequencing (NGS) data to provide sensitive and accurate variant calls for downstream analyses.

Key Features:

• Low-Coverage Optimization: Optimized for low-coverage scenarios (e.g., ~7X coverage) to enhance SNP detection where read depth is limited.
• Genotype-centric Calling: Performs genotype determination at each site and focuses calling on reliable positions to reduce false positives.
• Minor-allele Support Filtering: Excludes sites with unreliable minor-allele support, specifically those supported by only one read or located at read ends.
• Performance on RAD-seq: Achieves superior F-scores in low-coverage restriction-site associated DNA sequencing datasets from sorghum and rice individuals compared with existing tools.

Scientific Applications:

• Genome-wide association studies (GWAS): Improves the quality and sensitivity of variant datasets used for association mapping from low-coverage NGS data.
• Genomic prediction (GP): Enhances variant discovery for genomic prediction analyses where accurate SNP calls at low coverage benefit prediction models.

Methodology:

Aligns NGS reads to reference genome sequences and determines genotypes per site while excluding sites with insufficient minor-allele support (single-read support) or positional ambiguity at read ends prior to SNP calling.