Usage

Installation

Source code from Github :

$ git clone git@github.com:changlubio/GenomePrep.git

Setup

To use GenomePrep, first download relevant files:

$ make datadir
$ cd datadir
$ wget tp://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.75.dna.toplevel.fa.gz
$ gunzip Homo_sapiens.GRCh37.75.dna.toplevel.fa.gz
$ wget https://supfam.mrc-lmb.cam.ac.uk/GenomePrep/datadir/api.23andme.com
$ wget https://supfam.mrc-lmb.cam.ac.uk/GenomePrep/datadir/badalleles.dat
$ wget https://supfam.mrc-lmb.cam.ac.uk/GenomePrep/datadir/RS2GRCh37Orien_1.dat
$ wget https://supfam.mrc-lmb.cam.ac.uk/GenomePrep/datadir/THE_LIST.dat

Use liftOver for build other than GRCh37

$ wget ftp://hgdownload.cse.ucsc.edu/goldenPath/hg38/liftOver/hg38ToHg19.over.chain.gz
$ wget http://hgdownload.soe.ucsc.edu/goldenPath/hg18/liftOver/hg18ToHg19.over.chain.gz

Running test DNA

Run GenomePrep on a typical 23andMe file

$ cd ..
$ bin/process.py tutorial/testgenome.zip -d ./datadir -o ./outputs -i vcfindex