DNPcall

DNPcall genotypes double nucleotide polymorphisms (DNPs) from pileup files generated by samtools, leveraging read name information to reconstruct DNP genotypes and discriminate true DNPs from adjacent SNPs.

Key Features:

• Read-based genotype reconstruction: DNPcall uses read name information to reconstruct DNP genotypes at the individual level.
• Same-read coverage requirement: The genotype is called only when both positions of the DNP are covered by the same read, preventing spurious calls from sequencing errors.
• Discrimination of true DNPs from adjacent SNPs: DNPcall distinguishes DNPs arising from a single mutational event from two adjacent SNPs whose alternative variants are not linked on the same read.
• Extensibility to other variant types: The pipeline can be adapted to study other Multi Nucleotide Variants (MNVs) or microhaplotypes.

Scientific Applications:

• Human genome variation studies: DNPcall enables direct and reliable calling of DNP genotypes to study understudied genomic variants in the human genome.
• Genetic variation analysis: DNPcall enhances the study of genomic variation by accurately genotyping putative DNPs that consist of two adjacent variant nucleotides arising from a single mutational event.

Methodology:

DNPcall processes pileup files obtained with samtools and leverages read name information to reconstruct DNP genotypes when both positions of the DNP are covered by the same read.