README.md

Create an up to date OpenSNP community cohort from genome-wide genotyping data available on the OpenSNP platform

Dependency

The tools rely on a couple of dependencies. The versions mentioned were the one used on the last successful run

Dependencies in ./bin:

• bcftools and bgzip (from htslib) (1.5) http://www.htslib.org/download/ (included)
• liftOver (https://genome-store.ucsc.edu/) (free for academics, must be downloaded. Then see the 'Set the dependencies' part)
• unzip (UnZip 6.00 of 20 April 2009, by Debian.) (included)
• gunzip (gzip) 1.6 (included)
• plink (PLINK v1.90b4.5 64-bit) (included)
• vcf-sort (https://vcftools.github.io/license.html) (included)
• rename (The SZABÓ Gergely's version https://github.com/subogero/rename) (included)
• liftMap.py a script that use liftOver (https://genome.sph.umich.edu/wiki/LiftMap.py) (included)

Dependencies in ./ref are:

• hg18ToHg19.over.chain.gz (included)
• human_g1k_v37.fasta and human_g1k_v37.fai (http://www.internationalgenome.org/data-portal/search?q=%2Bhuman_g1k_v37.fasta) (downloaded if not present in ref at first exxecution)

Set the dependencies correctly:

• Either, make a link on each of the tools in the ./bin directories;
• Or edit the script to specify the location of the tool

Set the number of cores to use

• Edit the script to set the number of cores available by changing the value of variable nb_proc (default is 4)