PrepareRefGenomes.sh

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# Step 1 - Load the Conda environment from AnnotateVariants ##
##############################################################

MINI_CONDA_INSTALL_DIR=/mnt/common/WASSERMAN_SOFTWARE/AnnotateVariants/opt/miniconda3
source ${MINI_CONDA_INSTALL_DIR}/etc/profile.d/conda.sh
conda activate /mnt/common/WASSERMAN_SOFTWARE/AnnotateVariants/opt/AnnotateVariantsEnvironment

# Where do you want them
GENOME_DIR=/mnt/common/DATABASES/REFERENCES/
mkdir -p $GENOME_DIR
cd $GENOME_DIR


###############################################################################
# Step 2 - Get Reference genomes and index them. #
##################################################

# Get Reference Genome Files (these match the files in str_bams) 
## GRCh37
mkdir -p GRCh37
wget http://www.bcgsc.ca/downloads/genomes/9606/hg19/1000genomes/bwa_ind/genome/GRCh37-lite.fa
wget http://www.bcgsc.ca/downloads/genomes/9606/hg19/1000genomes/bwa_ind/genome/GRCh37-lite.fa.fai

bwa index GRCh37-lite.fa

## GRCh38
mkdir -p GRCh38
wget ftp://ftp.ensembl.org/pub/release-96/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz
gunzip -c Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz > GRCh38-lite.fa

samtools faidx GRCh38-lite.fa
bwa index GRCh38-lite.fa