OpenSNP-dendrogram

Phylogenetic tree generator for samples from OpenSNP. Tested on Ubuntu LTS 20.04 for Windows.

Packages to install

Shell

• htslib
• bgzip
• bcftools
• R-base

R

• gdsfmt, SNPRelate, ggplot2, dendextend, circlize

Data to install

1. Genome sequence, primary assembly (GRCh37) in .fa.gz format (download here: https://www.gencodegenes.org/human/release_39lift37.html)
2. 23andme SNP files in .23andme.txt format (download here: https://archive.org/details/opensnp_data_dumps)

How to run

Invoke from Ubuntu LTS shell: sh convert.sh

To-do list

1. Insert curl command to download and unpack datasets for OpenSNP and GRCh37
2. Insert install commands for libraries
3. Batch file renamer to shorten labels (e.g. "user6969_file420_yearofbirth..." to "user6969")
4. Additional code to clean OpenSNP/23andme data, and make cross-compatible between releases