USeq Source Code

MultiSampleVCFFilter
* Added option to filter by region
* Cleaned up chunking issues when no chunking is indicated
VarScanVCFParser
* New app to extract SOMATIC calls and replace QUAL score with the ssc score.
SamAlignmentExtractor
* Added option to output alignments that don't intersect the regions.
BamSurgeonMutator
* Generates random mutations in a list of regions for the BamSurgeon application
BisStat
* Fixed an issue where some runs were throwing a comparator contract sort error due to lack of data in a particular base context and thus null fraction values