TumorCNV is a tool designed to jointly detecting of germline and somatic copy number events from WGS data of the matched tumor-normal sample pair.
The easiest way to get TumorCNV is to download the binary distribution from the TumorCNV github release page. Alternatively, you can build TumorCNV from source with gradle.
- git clone --recursive https://github.com/yongzhuang/TumorCNV.git
- Install gradle build tool (https://gradle.org/)
- cd TumorCNV
- gradle build
You'll find the executable jar file in TumorCNV/build/libs/.
If you want to run TumorCNV, you'll need:
- Install Java SE Development Kit 8
- Install R (Rscript exectuable must be on the path)
- Install Runiversal (https://cran.r-project.org/web/packages/Runiversal/index.html), VGAM (https://cran.r-project.org/web/packages/VGAM/index.html) and qcc(https://cran.r-project.org/web/packages/qcc/) package in R
usage: java -jar TumorCNV.jar [OPTIONS]
1. preprocess
This option is used to extract the information from the normal and tumor BAM files.
usage: java -jar TumorCNV.jar preprocess [OPTIONS]
-referenceSequenceFile reference genome file (required)
-normalVCFFile normal sample's vcf file (optional)
-normalBAMFile normal sample's bam file (required)
-tumorBAMFile tumor sample's bam file (required)
-mappabilityFile mappability file (required)
-outputPrefix prefix of output file (required)
-windowSize window size (optional, default 500)
-minMappingQuality minimum mapping quality (optional, default 1)
-minBaseQuality minimum base quality (optional, default 20)
2. call
This option is used to jointly call germline and soamtic CNVs.
usage: java -jar TumorCNV.jar call [OPTIONS]
-rdFile read depth file (required)
-afFile allele frequency file (optional)
-mappabilityFile mappability file (required)
-outputFile prefix of toutput file (required)
-exclude exclude regions
-transitionProb transition probability of different states (optional, default 0.00001)
-minMappability minimum mappability of window (optional, default 0.3)
-minDisatance minimum distance to merge adjacent CNVs (optional, default 10000)
-purity tumor purity (optional, default 1.0)
-ploidy tumor ploidy (optional, default 2)
-outlier the percentage of outliers (optional, default 0.1)
-nt number of threads (optional, default 1)
The sample data sets and script can be found at http://182.92.97.240/exchange/190419/example.zip, and the users need to download the reference genome file (ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz) and mappability file (http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeMapability/wgEncodeCrgMapabilityAlign100mer.bigWig).