run Control-FREEC

Control-FREEC.sh

sudo apt update
sudo apt install -y r-base-dev

# ubuntu 18.04 works, 16.04 needs download from https://dlang.org/download.html
sudo apt install -y ldc

git clone --recursive https://github.com/biod/sambamba.git -b v0.6.8
cd sambamba
make -j $(nproc)

git clone https://github.com/BoevaLab/FREEC.git -b v11.5
cd FREEC/src
make -j $(nproc)

# download
# https://xfer.curie.fr/get/nil/7hZIk1C63h0/hg19_len100bp.tar.gz
# https://xfer.curie.fr/get/nil/vyIi4w8EONl/out100m2_hg38.zip
# https://xfer.curie.fr/get/nil/n5jk4aipGAr/hg19_snp142.SingleDiNucl.1based.txt.gz

tar axvf hg19_len100bp.tar.gz
unzip out100m2_hg38.zip
gunzip -k hg19_snp142.SingleDiNucl.1based.txt.gz
cat hg19_snp142.SingleDiNucl.1based.txt | awk {'printf ("%s\t%s\t%s\n", $1,$2-1,$2)'} >hg19_snp142.SingleDiNucl.1based.bed

freec -conf config_chr19.txt

cat makeGraph_Chromosome.R | R --slave --args 19 2 chr_19.noDup0.pileup.gz_ratio.txt chr_19.noDup0.pileup.gz_BAF.txt