The Critical Role of Choosing Appropriate Genotype Caller and Reference Genome for Population Genomic Inference: A Demonstration Study with Five Pterocarya Species

Abstract excerpt

Contemporary population genomic studies typically involve mapping raw reads to a reference genome and analyzing single nucleotide polymorphism (SNP) data obtained from variant calling. Despite the widespread use of the genotype caller GATK for variant calling, its design primarily for human data poses limitations in non-human species. Recently, ATLAS has emerged as a promising alternative caller, exhibiting superi...

Topics

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• Chromosome Mapping
• Gene Frequency
• Genetics, Population
• Genotype
• High-Throughput Nucleotide Sequencing
• Likelihood Functions
• Models, Genetic
• Polymorphism, Single Nucleotide

Identifiers and source

Literature Corpus work

2bcb44c5-14fc-5836-9b43-f4beffe67de7

DOI

10.22541/au.171429776.63133124/v1