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H2/H1 and H12

JS James Sweet-Jones
VL Vasileios Panagiotis Lenis
AY Andrey A. Yurchenko
NY Nikolay S. Yudin
MS Martin Swain
DL Denis M. Larkin
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Autosomal SNPs were filtered for –maf 0.0000001 –geno 0.1 –mind 0.1 by Plink. SNPs were then phased by chromosome using ShapeIt2 (Delaneau et al., 2011) with 400 states and an effective population size of 100. Phased chromosomes were split into appropriate groupings per chromosome using Plink and H2/H1, H12 were calculated using the H1_H12.py Python script (Garud et al., 2015). H2/H1 and H12 values were calculated in windows of 25 SNPs using a step size of one SNP following our previous study (Yurchenko et al., 2019).

Copyright and License information:  ©2021 Sweet-Jones, Lenis, Yurchenko, Yudin, Swain and Larkin.
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