@@ -11,9 +11,10 @@ that users understand how the changes affect the new version.
version 1.0.0-dev
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+ Mutect2: Add GATK tasks related to variant filtering (LearnReadOrientationModel, MergeStats, GetPileupSummaries, CalculateContamination and FilterMutectCalls)
+ GATK: Add CombineVariants task that allows, e.g., to merge VCFs from different callers.
+ Mutect2: Add GATK tasks related to variant filtering (LearnReadOrientationModel, MergeStats, GetPileupSummaries, CalculateContamination and FilterMutectCalls).
+ Mutect2: Add "--germline-resource" and "--f1r2-tar-gz" inputs, requiring an update to GATK 4.1.2.0.
+ Mutect2: Add necessary missing index attribute for panel of normals
+ Mutect2: Add necessary missing index attribute for panel of normals.
+ VarDict: Add user definable flags (-M, -A, -Q, -d, -v, -f) to the paired VCF filtering script.
+ Cutadapt: If the output is a gzipped file, compress with level 1 (instead of default 6).
+ Cutadapt: Fix issues with read2output when using single-end reads.
