Examples#
This section contains example analyses of local ancestry inference performed on admixed populations from the 1000 Genomes Project. Below, we provide a detailed description of data, preprocessing steps, links to the examples, and the considered demographic models.
Data#
Dataset description
Description of the local ancestry datasets used in the examples (1000 Genomes Project).
Data processing
Preprocessing and formatting steps applied to the data.
Example analyses#
ASW population
Example analyses for the ASW population.
Demographic models#
In this section, we consider three demographic models of varying complexity. The corresponding YAML files are specified below.
One pulse model#
The following model is written in the file ppp.yaml.
model_name: One pulse
description: Represents a population X founded t generations ago by EUR, NAT, and AFR.
time_units: generations
demes:
- name: EUR
- name: AFR
- name: NAT
- name: X
ancestors: [EUR, NAT, AFR]
proportions: [REUR, RNAT, RAFR]
start_time: t
Two pulses model#
The following model is written in the file ppp_pxx.yaml.
model_name: Two pulses
description: A population X founded t1 generations ago by EUR, AFR, and NAT, then subsequent EUR migration.
time_units: generations
demes:
- name: EUR
- name: AFR
- name: NAT
- name: X
ancestors: [EUR, NAT, AFR]
proportions: [REUR, RNAT, RAFR]
start_time: t1
pulses:
- sources: [EUR]
dest: X
proportions: [REUR2]
time: t2
Three pulses model#
The following model is written in the file ppp_xxp_pxx.yaml.
model_name: Three pulses
description: A demes model with flexible parameters. Represents a population X founded t1 generations ago by EUR and NAT, then subsequent AFR migration,
then subsequent EUR migration.
time_units: generations
demes:
- name: EUR
- name: NAT
- name: targetpop
ancestors: [EUR, NAT]
proportions: [REUR, RNAT]
start_time: t1
pulses:
- sources: [AFR]
dest: targetpop
proportions: [RAFR]
time: t2
- sources: [EUR]
dest: targetpop
proportions: [REUR2]
time: t3