Changes in version 1.8.1 ------------------------ o Fixes a crash when gc.gene.file listed multiple symbols per exon (https://github.com/lima1/PureCN/issues/16) Changes in version 1.8.0 ------------------------ NEW FEATURES o Support for off-target reads in copy number normalization and segmentation o Added mutation burden calculation o More robust mapping bias estimation o Added support for CNVkit coverage files (*.cnn, *.cnr) o IntervalFile.R can annotate targets with gene symbols and automatically convert chromosome naming styles o Better artifact filtering by using normalDB more efficiently o Support for mappability scores o Coverage calculation can now include duplicates o calculateBamCoverageByInterval now provides fragment counts and duplication rates o findBestNormal pooling now fragment count based, not coverage based o Experimental support for GATK4 o predictSomatic now reports posterior probabilites of minor segment copy numbers, flags segments if copy numbers are unreliable o Targets can be annotated with multiple gene symbols (comma separated) o Code cleanups (switch to GRanges where possible, switch to optparse in command line tools) API CHANGES o Due to novel optimizations of provided bait intervals, we highly recommend to regenerate the interval files and normal databases and recalculate all coverages from BAM files o New functions: annotateTargets, callMutationBurden o Defunct functions: createSNPBlacklist, getDiploid, autoCurateResults, readCoverageGatk o min.normals defaults to 2 (changed from 4) in setMappingBiasVcf o normalDB.min.coverage defaults to 0.25 (changed from 0.2) in filterTargets o log.ratio.calibration defaults to 0.1 (from 0.25) in runAbsoluteCN; now relative to purity, not log-ratio noise o Removed gc.data from filterTargets since gc_bias is now added to tumor coverage o dropped purecn.output from correctCoverageBias (no two-pass anymore) o Coverage.R argument --gatkcoverage renamed to --coverage o Dropped GC-normalization functionality in NormalDB, since this is now conveniently done in Coverage.R o Renamed PureCN.R --outdir argument to --out. Can now specify a file prefix as in GATK. Filenames are thus not forced to sample id anymore. If --out is a directory, it will behave like before and will use out/sampleid_suffix as filename.