DNPcall: a new pipeline for accurate double nucleotide polymorphism calling

Area of Science:

• Genomics
• Human Genetics
• Bioinformatics

Background:

• Double Nucleotide Polymorphisms (DNPs), comprising two adjacent variant nucleotides from a single mutation, are understudied genomic variants.
• Existing methods lack direct and reliable individual-level DNP genotype calling, hindering genetic variation studies.

Purpose of the Study:

• To introduce DNPcall, a novel pipeline for accurate genotyping of Double Nucleotide Polymorphisms (DNPs).
• To enable reliable individual-level DNP genotype calls, distinguishing single mutations from adjacent SNPs.

Main Methods:

• DNPcall utilizes samtools-generated pileup files.
• It reconstructs DNP genotypes by leveraging read name information, ensuring both positions are covered by the same read.
• This approach filters out sequencing errors and differentiates true DNPs from linked single nucleotide polymorphisms (SNPs).

Main Results:

• DNPcall accurately genotypes putative DNPs at the individual level.
• The pipeline effectively distinguishes DNPs arising from single mutations versus two independent SNPs.
• It provides a reliable method for calling DNP genotypes, overcoming limitations of previous approaches.

Conclusions:

• DNPcall is a user-friendly pipeline that enhances the study of genomic variation.
• The pipeline can be adapted for genotyping other Multi Nucleotide Variants (MNVs) and microhaplotypes.
• Source code and documentation are publicly available, facilitating broader research application.