#TrioCNV #Introduction TrioCNV is a tool designed to jointly detecting CNVs from WGS data in parent-offspring trios. It models read depth signal with the negative binomial regression to accommodate over-dispersion and considered GC content and mappability bias. It leverages parent-offspring relationship to apply Mendelian inheritance constraint while allowing for the rare incidence of de novo events. It uses a hidden Markov model (HMM) by combining the two aforementioned models to jointly perform CNV segmentation for the trio. #Installation If you want to run TrioCNV, you'll need:
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Java 1.7+
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Apache Maven (if you want to build the source)
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R (Rscript exectuable must be set in the PATH environment variable)
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Runiversal package(http://cran.rproject.org/web/packages/Runiversal/index.html) in R environment
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The easiest way to get TrioCNV is to download the binary distribution from the TrioCNV github release page. Alternatively, you can build TrioCNV from source with Maven.
git clone --recursive https://github.com/yongzhuang/TrioCNV.git
cd TrioCNV/
mvn clean install -Dmaven.compiler.source=1.7 -Dmaven.compiler.target=1.7
#Running
usage: java -jar TrioCNV.jar [OPTIONS]
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preprocess
This command is to extract the information from the BAM file.
usage: java -jar TrioCNV.jar preprocess [OPTIONS] -R,--reference <FILE> reference genome file (required) -B,--bams <FILE> bam list file (required) -P,--pedigree <FILE> pedigree file (required) -M,--mappability <FILE> mappability file (required) -O,--output <FILE> perfix of output file (required) --window <INT> window size (optional, default 200) --min_mapping_quality <INT> minumum mapping quality (optional,default 0)
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call
This command is to jointly call CNVs from a parent-offspring trio.
usage: java -jar TrioCNV.jar call [OPTIONS] -I,--input <FILE> read count file got by the preprocess step (required) -P,--pedigree <FILE> pedigree file (required) -M,--mappability <FILE> mappability file (required) -O,--output <FILE> output structural variation file (required) --min_mappability <FLOAT> minumum mappability(optional, default 0) --mutation_rate <FLOAT> de novo mutation rate (optional, default 0.0001) --transition_prob <FLOAT> probability of transition between two different copy number states(optional, default 0.00001) --outlier <FLOAT> the predefined percentage of outliers (optional, default 0.025) --min_distance <INT> minumum distance to merge two adjacent CNVs (optional, default 10K) --nt <INT> number of threads (optional, default 1) --gc_bin_size <INT> size of gc bin by percent (optional, default 1)
#File Instruction
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bam list file (one columns)
Column 1: path of .bam file
Example:
/path/Sample1.bam /path/Sample2.bam /path/Sample3.bam ...
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pedigree file
See (http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml)
Note: The Individual ID must be same as the @RG SM tag of the bam file.
#Contact [email protected]