Repo for exploratory analysis on 1000 Genomes Project data.
Maintained by Christian Porras at the University of Chicago.
References:
- Novembre et al (https://www.nature.com/articles/nature07331)
- Popres (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2556436/)
- 1000 Genomes (https://www.nature.com/articles/nature15393/figures/1)
- 1000 Genomes PCA (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3701331/)
- SNP coding bias (https://www.biorxiv.org/content/biorxiv/early/2018/08/16/393611.full.pdf?fbclid=IwAR3hFYBFB18IwAziMPejCN7nfe9-7NCa1ENcmra_vJ7fOOKNtPM3cknX2wo)
- PCA with simulations (https://journals.plos.org/plosgenetics/article?id=10.1371%2Fjournal.pgen.1000686&fbclid=IwAR389fIaG3aBUs9U7e9oZiF3NWdcBERgtUkstgR7eNb9I5aHWrW3MQKxAjI)
- Spatial PCA with simulations (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3989108/)
- Spatial sampling (https://www.biorxiv.org/content/10.1101/004713v1.full)
- Spatial ancestry (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4184261/)
// Useful tools
- scikit-allel (https://scikit-allel.readthedocs.io/en/stable/?fbclid=IwAR2DoVWFH1szVNfBUnrPhTfbn4eRUPxhuIJfxzsjDHRZ1h4gaUqHyW3ZKsU)
- 1000 genomes data (ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/technical/working/)
- SNP coding example worksheet (https://botany.natur.cuni.cz/hodnocenidat/Lesson_05_tutorial.pdf)
- 1000 genomes PCA example (https://bwlewis.github.io/1000_genomes_examples/PCA.html)
- Pop structure PCA (https://privefl.github.io/bigsnpr/articles/how-to-PCA.html)