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A curious research on my genotype data from 23andMe
Shell Python R
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2.convert_to_ped.py
3.add_fake_sample_ped.py
3.run.impute.sh
4.compile.sh
5.plot.R
README.md
impute2.py
overall.sh
plot_imputation.R

README.md

23andme_research

This is a curiosity driven project to impute my 23andme data using 1000 Genomes project.

The scripts work sequentially as suggested by the numbers, the overall.sh has information of the 1st step.

Future to-do list:

Run EIGENSOFT to compute PCs using overlapping variants between my genotype and 1000G genotypes

Plot PCA plot to visualize genetic popluation assignment

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