Package net.sf.varscan

Class Summary
CallMpileup A class for calling variants or consensus bases from a pileup file
CallPileup A class for calling variants or consensus bases from a pileup file
Comparison A class for comparing positions (variants) between two files
CopyCaller A DEPRECATED class for calling copy number variants from somatic copynumber output
Copynumber  
Coverage A class for assessing coverage of target regions (experimental)
FilterSomatic A class for filtering VarScan variant predictions
FilterVariants A class for filtering VarScan variant predictions
FishersExact A statistical class for performing Fisher's exact test.
LimitVariants A class for restricting a list of variants to a given set of positions or regions
ProcessSomatic A class for processing VarScan output by somatic status and confidence
ReadCounts A class for obtaining read counts for a list of variants
Somatic A class for determining somatic status of variants from Normal/Tumor pileup files
VarScan A set of tools for variant detection in next-generation sequence data.