Diversity and recent selection on Amylase structural haplotypes in human populations

A repo for code and methods related to analyses and figures. This code is deposited under the GNU General Public License, version 3.0 (GPL-3.0). All code is written for python 3 or R version 4 unless otherwise indicated. There are no operating system requirements.

Table of contents

Coalescent tree

Ancestral state reconstruction

PCA with the flanking sequence

Trio-based recombination rate visualization

Variant effect prediction

Population genetics of flanking loci

Read depth genotyping

Graph genotyping

Assess graph genotypes (including selection analyses)

Expression analyses

PGGB variation graph

PGRTK pangenome graph construction

Assess AMY structures