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.

1. git clone --recursive https://github.com/yongzhuang/TumorCNV.git
2. Install gradle build tool (https://gradle.org/)
3. cd TumorCNV
4. gradle build

You'll find the executable jar file in TumorCNV/build/libs/.

If you want to run TumorCNV, you'll need:

1. Install Java SE Development Kit 8
2. Install R (Rscript exectuable must be on the path)
3. 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).

[email protected]

MIT