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C

CallMpileup - Class in net.sf.varscan
A class for calling variants or consensus bases from a pileup file
CallMpileup(String[], String) - Constructor for class net.sf.varscan.CallMpileup
 
CallPileup - Class in net.sf.varscan
A class for calling variants or consensus bases from a pileup file
CallPileup(String[], String) - Constructor for class net.sf.varscan.CallPileup
 
compare(String[], HashMap<String, String>) - Static method in class net.sf.varscan.VarScan
Compares two lists of positions/variants
Comparison - Class in net.sf.varscan
A class for comparing positions (variants) between two files
Comparison(String[]) - Constructor for class net.sf.varscan.Comparison
 
CopyCaller - Class in net.sf.varscan
A DEPRECATED class for calling copy number variants from somatic copynumber output
CopyCaller(String[], HashMap<String, String>) - Constructor for class net.sf.varscan.CopyCaller
 
copyCaller(String[], HashMap<String, String>) - Static method in class net.sf.varscan.VarScan
Calls somatic copy number events from copynumber output
Copynumber - Class in net.sf.varscan
 
Copynumber(String[], boolean) - Constructor for class net.sf.varscan.Copynumber
 
Copynumber(String[]) - Constructor for class net.sf.varscan.Copynumber
 
copynumber(String[], HashMap<String, String>) - Static method in class net.sf.varscan.VarScan
Determines tumor copy number from normal and tumor pileup files
Coverage - Class in net.sf.varscan
A class for assessing coverage of target regions (experimental)
Coverage(String[]) - Constructor for class net.sf.varscan.Coverage
 
coverage(String[], HashMap<String, String>) - Static method in class net.sf.varscan.VarScan
Reports region coverage from a BAM file

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