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INSTALL
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INSTALL
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Building, Installing and Running CNVnator
=========================================
Requirements
============
Building CNVnator requires at least the following:
GNU make
C compiler (e.g. gcc or clang)
CERN ROOT (https://root.cern.ch)
samtools with HTSlib
GNU readline library
You must install ROOT package and set up $ROOTSYS variable (see ROOT documentation
https://root.cern.ch/root/html534/guides/users-guide/GettingStarted.html).
Download last samtools release https://github.com/samtools/samtools/releases and
compile samtools and HTSlib.
GNU readline library is required. You can install it using following commands:
yum install readline-devel # RPM-based systems
apt-get install libreadline-dev # Debian-based systems
or follow instructions: https://tiswww.case.edu/php/chet/readline/rltop.html
Building
========
Download last CNVnator release v0.4.1:
https://github.com/abyzovlab/CNVnator/releases/download/v0.4.1/CNVnator_v0.4.1.zip
Unzip and compile:
unzip CNVnator_v0.4.1.zip
cd CNVnator_v0.4.1
cd src
ln -s <path_to_samtools_dir> samtools
make OMP=no # without parallel support
or
make # with parallel suport
or
make LIBS="-lcrypto" # if you got compilation time error related to undifined libcrypto reference.
Installing
==========
Add CNVnator_v0.4.1/src folder to $PATH by adding following line to .bash_profile:
export PATH=<path_to_CNVnator_v0.4.1>/src:$PATH
or create symbolic links in folder that is already in $PATH (e.g. ~/bin/):
cd <local_bin_folder>
ln -s <path_to_CNVnator_v0.4.1>/src/cnvnator
ln -s <path_to_CNVnator_v0.4.1>/src/plotcircular.py
ln -s <path_to_CNVnator_v0.4.1>/src/plotrdbaf.py
ln -s <path_to_CNVnator_v0.4.1>/src/plotbaf.py
ln -s <path_to_CNVnator_v0.4.1>/src/pytools
Running
=======
* Extract read mapping:
cnvnator -root file.root -tree file.bam
or
cnvnator -root file.root -tree file.bam -chrom $(seq 1 22) X Y
or
cnvnator -root file.root -tree file.bam -chrom $(seq -f "chr%g" 1 22) chrX chrY
* Generate histogram:
cnvnator -root file.root -his 1000 -fasta reference_genome.fasta.gz
* Calculate statistics
cnvnator -root file.root -stat 1000
* Partition
cnvnator -root file.root -partition 1000
* Call CNVs
cnvnator -root file.root -call 1000
* Import SNP data
cnvnator -root file.root -vcf file.vcf.gz
* Import mask data
cnvnator -root file.root -mask mask.fa.gz
For hg19 reference genome mask file is provaded with CNVnator:
CNVnator_v0.4.1/ExampleData/20141020.strict_mask.whole_genome.fasta.gz
* Generate SNP histograms
cnvnator -root file.root -baf 10000
* List root file content
cnvnator -root file.root -ls
* Copy RD and SNP data to new root file
cnvnator -root file.root -cptrees new_file.root
* Genotype genomic regions - interactive mode
cnvnator -root file.root -genotype bin_size
* Ploting - interactive mode
cnvnator -root file.root -view 1000
* Ploting RD and BAF whole genome circular plots using python tool:
plotcircular.py file.root
all options:
plotcircular.py [-chrom CHROMOSOMES] [-bs BINSIZE] [-o SAVE_FILE]
[-t TITLE] [-rdbs RDBINSIZE] [-pbs PLOTBINSIZE]
[-nomask] [-useid] root_file
* Ploting RD and BAF signal over genomic region using python tool:
plotrdbaf.py file.root 15:1000000-5000000
all options:
plotrdbaf.py [-h] [-bs BINSIZE] [-rdbs RDBINSIZE] [-res RESOLUTION]
[-o SAVE_FILE] [-t TITLE] [-nomask] [-useid]
root_file region
* Ploting BAF signal over genomic region using python tool:
plotbaf.py file.root 15:1000000-5000000
all options:
plotbaf.py [-h] [-bs BINSIZE] [-rdbs RDBINSIZE] [-res RESOLUTION]
[-o SAVE_FILE] [-t TITLE] [-nomask] [-useid]
root_file region