A Cautionary Note on the Use of Genotype Callers in Phylogenomics.
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State: Public
Version: Final published version
License: CC BY-NC 4.0
State: Public
Version: Final published version
License: CC BY-NC 4.0
Serval ID
serval:BIB_BE78FE659A7E
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
A Cautionary Note on the Use of Genotype Callers in Phylogenomics.
Journal
Systematic biology
ISSN
1076-836X (Electronic)
ISSN-L
1063-5157
Publication state
Published
Issued date
16/06/2021
Peer-reviewed
Oui
Editor
Jermiin Lars
Volume
70
Number
4
Pages
844-854
Language
english
Notes
Publication types: Journal Article ; Research Support, Non-U.S. Gov't
Publication Status: ppublish
Publication Status: ppublish
Abstract
Next-generation-sequencing genotype callers are commonly used in studies to call variants from newly sequenced species. However, due to the current availability of genomic resources, it is still common practice to use only one reference genome for a given genus, or even one reference for an entire clade of a higher taxon. The problem with traditional genotype callers, such as the one from GATK, is that they are optimized for variant calling at the population level. However, when these callers are used at the phylogenetic level, the consequences for downstream analyses can be substantial. Here, we performed simulations to compare the performance between the genotype callers of GATK and ATLAS, and present their differences at various phylogenetic scales. We show that the genotype caller of GATK substantially underestimates the number of variants at the phylogenetic level, but not at the population level. We also found that the accuracy of heterozygote calls declines with increasing distance to the reference genome. We quantified this decline and found that it is very sharp in GATK, while ATLAS maintains high accuracy even at moderately divergent species from the reference. We further suggest that efforts should be taken towards acquiring more reference genomes per species, before pursuing high-scale phylogenomic studies. [ATLAS; efficiency of SNP calling; GATK; heterozygote calling; next-generation sequencing; reference genome; variant calling.].
Keywords
Genomics, Genotype, Genotyping Techniques, High-Throughput Nucleotide Sequencing, Phylogeny, Polymorphism, Single Nucleotide
Pubmed
Web of science
Open Access
Yes
Create date
26/10/2020 14:32
Last modification date
25/01/2024 8:43