bcbio b37/b38 WES/WGS

gistfile1.txt

# Install bcbio

mkdir bcbio
cd bcbio
wget https://raw.github.com/bcbio/bcbio-nextgen/master/scripts/bcbio_nextgen_install.py
mkdir data tooldir
python bcbio_nextgen_install.py data --tooldir=tooldir \
  --genomes GRCh37 --aligners bwa --aligners bowtie2
cd ../

# WGS b37

mkdir -p NA12878-trio-eval/config NA12878-trio-eval/input NA12878-trio-eval/work
cd NA12878-trio-eval/config
wget https://raw.github.com/bcbio/bcbio-nextgen/master/config/examples/NA12878-trio-wgs-validate.yaml
cd ../input
wget https://raw.github.com/bcbio/bcbio-nextgen/master/config/examples/NA12878-trio-wgs-validate-getdata.sh
bash NA12878-trio-wgs-validate-getdata.sh
cd ../work
bcbio_nextgen.py ../config/NA12878-trio-wgs-validate.yaml -n 16

# WGS hg38
mkdir -p NA12878-hg38-val
cd NA12878-hg38-val
wget https://raw.github.com/bcbio/bcbio-nextgen/master/config/examples/NA12878-hg38-validate-getdata.sh
bash NA12878-hg38-validate-getdata.sh
mkdir -p work
cd work
bcbio_nextgen.py ../config/NA12878-hg38-validate.yaml -n 16


# WES b37

mkdir -p NA12878-exome-eval
cd NA12878-exome-eval
wget https://raw.github.com/bcbio/bcbio-nextgen/master/config/examples/NA12878-exome-methodcmp-getdata.sh
bash NA12878-exome-methodcmp-getdata.sh
cd work
bcbio_nextgen.py ../config/NA12878-exome-methodcmp.yaml -n 8
https://www.ncbi.nlm.nih.gov//bioproject/PRJNA323611