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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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