Changes in version 1.2.3 ------------------------ - Critical fix for bug in setMappingBiasVcf. Somatic mutations were not excluded. This bug results in a too large mapping bias estimate and very wrong calls in hyper-mutated samples. Only affects matched tumor/normal pairs. - Un-deprecated segmentationPSCBS for panels with copy number tiling probes. Changes in version 1.2.2 ------------------------ - Fix for rare crash in very heterogeneous samples - Clarified interval padding in the vignette. - Un-deprecated segmentationPSCBS. Changes in version 1.2.1 ------------------------ - Fix for floating point overflow when iterations was set to a high value (https://support.bioconductor.org/p/88053/) - Fix for bug in callAlterationsFromSegmentation (resulting in wrong gene.mean, gene.max, gene.min values) - Check for overlapping intervals in readCoverageGatk Changes in version 1.2.0 ------------------------ Focus on PureCN 1.2 was to dramatically improve user-friendliness: - GATK requirement was dropped: PureCN now comes with functionality to generate coverage data when GATK is not available. - Experimental support for VCFs generated by other callers than MuTect 1.1.7 - Experimental automatic curation of results. - Output plots were polished. - Both numerical (NCBI-style) and non-numerical (UCSC-style) chromosome names (1 vs. chr1) supported. - Better integration into existing copy number pipelines. - Automatic COSMIC annotation. - Thorough checks of input data, resulting in fewer crashes with unhelpful error messages. - Documentation improvements. OTHER MAJOR ENHANCEMENTS - More thorough initial grid search should minimize cases where purity/ploidy is wrong because the solution was not considered. - More robust and accurate likelihood model that provides robust estimates of minor segment copy numbers and more accurate LOH. - Support for SNVs outside the target interval file (remove.off.target.snvs=FALSE). - Improved segmentation and log-ratio normalization. - Support for non-human samples. - Support for 100% pure samples (matched normal mode only). - Faster SNV fitting. - Experimental support for correcting non-reference mapping bias. API CHANGES - New functions: autoCurateResults, bootstrapResults, calculateBamCoverageByInterval, calculateGCContentByInterval, calculateLogRatio, calculatePowerDetectSomatic, callAlterations, callAlterationsFromSegmentation, callLOH, filterTargets, getDiploid, getSexFromVcf, setMappingBiasVcf - Deprecated functions: segmentationPSCBS - Renamed functions: createExonWeightFile to createTargetWeights - Renamed function arguments: exon.weight.file to target.weight.file gatk.normal.file to normal.coverage.file gatk.tumor.file to tumor.coverage.file coverage.cutoff to min.coverage - Changed defaults: findFocal: made defaults less stringent, now 3Mb (instead of 2Mb) and minimum copy number of 5 (callAlterations still uses 6 as default). runAbsoluteCN(genome): no default anymore (instead of 'hg19') OTHER NEW FEATURES - Functions to calculate power to detect mono-clonal and sub-clonal somatic mutations (Carter et al., Nature Biotech, 2012) were added. PLANNED FEATURES FOR PURECN 1.4 (BIOCONDUCTOR 3.5) - Support for indels. - Better runtime performance by ignoring unlikely solutions early. - Better support for known, small deletions and amplifications (e.g. EGFRvIII, MYC) - Better support for pool of normals. - Switch to S4 data structures (maybe). - Whole dataset visualizations (maybe).