read_haps

read_haps detects same-species contamination in short-read whole genome sequencing (WGS) data by identifying instances of three haplotypes between polymorphic single nucleotide polymorphisms (SNPs) in diploid organisms such as humans.

Key Features:

• Contamination detection: Detects contamination from other individuals of the same species by identifying unexpected haplotype patterns in sequencing data.
• Haplotype analysis: Identifies occurrences of three distinct haplotypes between polymorphic SNPs, leveraging the expectation of two haplotypes in diploid organisms.
• Short-read whole-genome sequencing support: Operates on short-read whole genome sequencing (WGS) data common in genomic studies.

Scientific Applications:

• Genetic research integrity: Ensures sample purity to support validity and reproducibility of genetic analyses.
• Disease studies: Maintains data integrity in clinical genetics and disease association studies by identifying contaminated samples.
• Population genetics: Verifies that samples accurately represent intended populations by detecting cross-sample contamination.

Methodology:

Analyzes sequencing reads for the presence of three haplotypes between polymorphic SNPs, where detection of a third haplotype indicates contamination in diploid organisms that are expected to exhibit two haplotypes.