DNPcall: a new pipeline for accurate double nucleotide polymorphism calling.

ABSTRACT:

Motivation

Among the genomic variants of the human genome, Double Nucleotide Polymorphisms (DNPs) are still understudied. They consist of two adjacent variant nucleotides that arise from a single mutational event. Despite their potential relevance in the study of genetic variation, no method currently exists to directly and reliably call DNP genotypes at the individual level.

Results

We present DNPcall, a new pipeline for accurately genotyping putative DNPs based on the pileup file obtained with samtools. DNPcall leverages the information about the read name to finely reconstruct the genotype of the DNPs at the individual level. The genotype is called when both positions of the DNPs are covered by the same read, ensuring that no spurious calls due to sequencing errors are in

SUBMITTER: Pistacchia L 

PROVIDER: S-EPMC12502915 | biostudies-literature | 2025

REPOSITORIES: biostudies-literature