A Cautionary Note on the Use of Genotype Callers in Phylogenomics

Details

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
Author(s)
Duchen Pablo, Salamin Nicolas
ISSN
1063-5157
1076-836X
ISSN-L
1063-5157
Publication state
Published
Issued date
21/10/2020
Peer-reviewed
Oui
Editor
Jermiin Lars
Language
english
Notes
Publication types: Journal Article
Publication Status: aheadofprint
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 a 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.
Keywords
Genetics, Ecology, Evolution, Behavior and Systematics
Pubmed
Open Access
Yes
Create date
26/10/2020 14:32
Last modification date
06/02/2021 7:26
Usage data