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