CNVision

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Welcome to CNVision

This program was designed and written by Stephan Sanders and Chris Mason from the State Lab at Yale University. It is designed to simplify all stages of predicting and analyzing CNVs, from running prediction algorithms and combining their results to visualizing the raw data and designing qPCR primers for confirmation.

If this is the first time you have used CNVision then check the CNVision basics for a quick overview.

Downloading CNVision

CNvision can be downloaded from SourceForge.net at this address:

https://sourceforge.net/projects/cnvision/files/

Installing CNVision

For directions on installing CNVision see the CNVision install page

CNV Data

BeadStudio	Imports raw data and creates a new BeadStudio project
FinalReports	Converts a BeadStudio project into data that CNVision can analyze

CNV Pipeline

See Pipeline	Shows an image of the entire pipeline: CNVision Pipeline Map
Start	Initiates a Logfile and Sequence tracker file, also asks how many processors to use
Gender	Determines the gender of FinalReports by looking at chrX homozygosity
Quality	Checks FinalReports quality by counting the number of probes with extreme and wide logR values
Convert	Converts FinalReports into suitable input files for PennCNV and QuantiSNP
Input	Makes a list of all files made during the Convert function and prepares a list of files for PennCNV and a batch file for QuantiSNP
GNOSIS	Runs the GNOSIS CNV detection tool on all files with 'FinalReport' in their name
GNOSIS old	Runs a version of GNOSIS CNV detection tool that modifies LogR values on chrX and chrY for both sexes, this is not necessary for newer Illumina chips (1M Duo, 370 Quad, Omni)
RF GNOSIS	Reformats GNOSIS output to allow merging
PennCNV	Runs the PennCNV CNV detection tool on all files in the list created by Input
RF PennCNV	Reformats PennCNV output to allow merging
QuantiSNP	Runs the QuantiSNP CNV detection tool on all files in the batch file created by Input
RF QuantiSNP	Reformats QuantiSNP output to allow merging
Merge	Merges files in the Merge input format
Rare	Compares merged output to a list of common loci in the Annotation Folder
Bad	Combines lists of samples that failed quality control into a single list
Pedfile	Creates a modified pedfile without samples in the list generated by Bad
Denovo	Compares children to parents using a pedfile (with 'pedfile' in the filename)
Summary	Converts the Denovo output into a readable format and makes a UCSC genome browser file
Annotate	Annotates the Summary output for genes, common variants and regions of interest
Homodel	Finds homozygous deletions in FinalReports
RF Homodel	Reformats Homodel output to the Merge input format
Annotate	Annotates the Homodel output for genes, common variants and regions of interest
Clean	Removes any unnecessary files from the folder

Quality Control

Quality	Checks FinalReports quality by counting the number of probes with extreme and wide logR values
Family	Checks the family relationships of all FinalReports in a pedfile using PLINK
Order	Checks that all FinalReports are in the same order
Strand	Checks that all FinalReports are from the same strand
Overlap	Looks for overlap between regions or CNVs in a file

CNV Analysis

De Novo 2	A different method of de novo CNV prediction that uses the FinalReports and a pedfile to work out whether a list CNVs are de novo or inherited
Large	An algorithm for joining together large CNVs that have been made into smaller predictions with gaps
Recurrent	Works out the relative frequency of CNVs from two files of CNVs
Recurrent thres	Same as Recurrent, but filters the input by CNV type, number of algorithms and number of probes
Frequency	Determines the frequency of CNVs/regions across all samples
eTaqman	Examines all FinalReports for evidence of CNVs at specified co-ordinates
Loci	Reduces a list of regions/CNVs to non-overlapping loci
Compare	Compares the output of two algorithms/chips run on the same samples
Proportion	Calculates the number of CNVs and individuals meeting specified criteria to calculate CNV burden
Template	Creates a template for running Multiproportion
Multiproportion	Similar to Proportion, but can do numerous analyses. Use the Template function above to create a template specifiying the analyses to perform, add the analyses then run this function.

Annotation

Annotate	Annotates a list of regions (chr, start, stop) against a series of annotation files (eg genes); this function allows numerous analyses and can be customised using the Template function below
Template	Makes a custom annotation template of all the files in the Annotation Folder
Pedfile	Annotates a list of regions (chr, start, stop) against a pedfile to show family, gender and phenotype
Samples	Annotates a list of regions against a list of samples
Genes	Finds the chr, position, number of exons and gene name of each RefSeq Gene Symbol (eg NRXN1)
Genes2	Similar to Genes, but performs the analysis of the internet and is slower
SNPcount	Works out the number of probes in a FinalReports file within each region/CNV
dbSNP	Works out the number of common SNPs present in dbSNP within each region/CNV
SNP	Uses the internet to look up SNP 'rs' IDs in dbSNP and return chr and position

Visualization

CNVs	Makes a PDF of the LogR and BAF values for CNVs per family (SOR plot)
BEDgraph	Makes a UCSC genome browser custom track of Frequency files
Wiggle	Makes a UCSC genome browser custom track of large Frequency files
BEDfile	Makes a UCSC genome browser custom track of CNV files
FinalReport	Makes a UCSC genome browser custom track of a FinalReport

FinalReport Analysis

SampleID	Quickly finds the sample ID and chip type from FinalReports
Gender	Looks for 'FinalReport' and determines sample ID, chip type and sex
Ancestry	Uses 400 ancestry informative markers (AIMs) to determine connitent of origin
Mean LogR	Calculates the Mean, median and stdev in LogR of each chromosome
Consensus	Makes a list of the probes common to different chip types in FinalReports
Prune	Removes probes that are not present in the consensus list from Consensus out of FinalReports
PLINK	Converts FinalReports into PLINK input format (.ped and .map)
Homodel	Finds homozygous deletions in FinalReports
UPD	Calculates the percentage homozygosity per chromosome to detect uniparental disomy

File Manipulation

List	Makes a list of every file and folder
Copy	Copies files in a text file to a new folder
Move	Moves files in a text file to a new folder
vLookup	Looks up terms in a reference file to add a new column
Split	Looks for differences in a specified column and splits the file accordingly
Combine	Combines multiple files that have columns in the same order
Sort	Sorts the file by up to three columns
Columns	Changes the order of columns in a file
Trim top	Removes lines from the top of a file
Trim bottom	Removes lines from the bottom of a file (useful for making a testfile)
Duplicates	Removes duplicate lines in a file
Differences	Find differences between two files that should be identical

Other Tools

GC content	Calculates the GC content for a list of regions
Get DNA	Looks up the DNA sequence for a list of regions
Primers	Designs qPCR or PCR primers for a list of regions

Advanced Users

The graphical user interface (CNVision.jar) is not necessary for running the functions. The perl script Combined_CNVv1.73.pl can be used alone to perform all these functions using command prompt (Windows) or terminal (Mac and Linux). On the pages showing how a specific function is performed in CNVision, the command line description is also given.