Installation Coral

git clone --recursive https://github.com/tobiasrausch/coral.git

cd coral/

make all

Reference Bundle

You then need to download the reference bundle with mappability maps and 1000 Genomes SNPs (~737Mb).

Download Reference Bundle

tar -xzf referenceBundle.tar.gz

Running Coral

./src/coral call -v referenceBundle/GRCh37.snps.bcf -g GRCh37.fa -m referenceBundle/Homo_sapiens.GRCh37.dna.primary_assembly.fa.r101.s501.blacklist.gz -s <SampleName> -o <outprefix> -l <control.bam> <tumor.bam>

Segmentation plots you can generate using:

Rscript ./R/rd.R outprefix.adaptive.cov.gz outprefix.segment.gz

Germline/Somatic Copy-Number Calling

Work-in-progress