Detecting Runs of Heterozygosity in Genomics

From the VCF, Plink was used to generate .ped and .map files. (http://pngu.mgh.harvard.edu/purcell/plink/) [58 (link)]. To detect and characterize the stretches of heterozygosity the package “detectRUNS” in R was then used. (https://github.com/bioinformatics-ptp/detectRUNS/tree/master/detectRUNS). We used the function slidingRuns.run with the following parameters: WindowSize=10, threshold=0.05, RoHet=True, minDensity=1/100, rest as default.

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Jaegle B., Pisupati R., Soto-Jiménez L.M., Burns R., Rabanal F.A, & Nordborg M. (2023). Extensive sequence duplication in Arabidopsis revealed by pseudo-heterozygosity. Genome Biology, 24, 44.

Publication 2023

Heterozygosity Tree

Corresponding Organization :

Other organizations : Austrian Academy of Sciences, Vienna Biocenter, Gregor Mendel Institute of Molecular Plant Biology, Max Planck Institute for Developmental Biology

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Variable analysis

independent variables

WindowSize
Threshold
RoHet
MinDensity

dependent variables

Stretches of heterozygosity

control variables

Rest as default

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