C F G L M N P R S T V

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

callTrio(String, HashMap<String, String>, HashMap<String, String>, HashMap<String, String>, int, double, int, double, double) - Method in class net.sf.varscan.Trio

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 class for calling/GC-adjusting copy number variants from raw 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

A class for calling copy number variants between a tumor and a matched normal sample

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