pixy: Unbiased estimation of nucleotide diversity and divergence in the presence of missing data

Abstract

Population genetic analyses often use summary statistics to describe patterns of genetic variation and provide insight into evolutionary processes. Among the most fundamental of these summary statistics are π and dXY, which are used to describe genetic diversity within and between populations, respectively. Here, we address a widespread issue in π and dXY calculation: systematic bias generated by missing data of various types. Many popular methods for calculating π and dXY operate on data encoded in the variant call format (VCF), which condenses genetic data by omitting invariant sites. When calculating π and dXY using a VCF, it is often implicitly assumed that missing genotypes (including those at sites not represented in the VCF) are homozygous for the reference allele. Here, we show how this assumption can result in substantial downward bias in estimates of π and dXY that is directly proportional to the amount of missing data. We discuss the pervasive nature and importance of this problem in population genetics, and introduce a user‐friendly UNIX command line utility, pixy, that solves this problem via an algorithm that generates unbiased estimates of π and dXY in the face of missing data. We compare pixy to existing methods using both simulated and empirical data, and show that pixy alone produces unbiased estimates of π and dXY regardless of the form or amount of missing data. In summary, our software solves a long‐standing problem in applied population genetics and highlights the importance of properly accounting for missing data in population genetic analyses.

Signatures of mitonuclear coevolution in a warbler species complex

“…Signature of selective sweep within chr5 candidate region. To test for signatures of a selective sweep within the candidate gene block in the coastal STOW populations, we calculated nucleotide diversity (π) with pixy 72 and linkage equilibrium (LD) around the~1.2 Mb candidate gene block (see above) with VCFtools and the input being all the coast STOW samples. We calculated pair-wise LD as the squared correlation coefficient of genotypes with the '-geno-r2' command.…”

Genetic Divergence and Population Structure in Weedy and Cultivated Broomcorn Millets (Panicum miliaceum L.) Revealed by Specific-Locus Amplified Fragment Sequencing (SLAF-Seq)

“…Genetic diversity indices, including the observed heterozygosity ( H O ) and expected heterozygosity ( H E ) for weedy and cultivated broomcorn millets were calculated using VCFtools software ( Danecek et al, 2011 ). The analysis of nucleotide diversity (π) was performed using pixy 1.0.0 based on VCF data including invariant sites to avoid biased estimation ( Korunes and Samuk, 2021 ). A VCF file including invariant sites was generated in GATK 3.8 by using the “-allSites” flag in GenotypeGVCFs, with the filtering criteria set to “DP > = 5, GQ > = 40| RGQ > = 40” for invariant sites.…”

“…The LD decay graphs of both weedy and cultivated broomcorn millets were plotted. The nucleotide diversity (π) and the pairwise fixation index, i.e., F-statistics ( F ST ), across different groups (excluding the “mosaics”) were calculated using pixy ( Korunes and Samuk, 2021 ).…”

The genome of the zoonotic malaria parasite Plasmodium simium reveals adaptations to host-switching

“…To account for the differences in read coverage between samples we used the pixy software [77], which produces unbiased estimates of D XY in the presence of missing data. Population divergence (D XY ) was calculated from this all-site VCF using pixy version 1.0.4.beta1, either in 10 kb windows or in gene coordinate windows.…”