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Created with Raphaël 2.2.022Sep17161512111098532129Aug28272625222019181514121187654130Jul29282724232221181514327Jun26232119171312109654327May2621201514Added filter stepNow outputs a multi allelic vcf fileFix config name spaceAdded overlap metrics plotOutput files change to gz outputAdded known optionFix counting on big filesJoint variantcalling is now optionalChanged test filesAdded combine multisample variantcallingChange to sample fieldChange to biopet gatk modulesAdded CombineVariantsAdd output_mode optionAdded joint variantcalling stepFunction for gvcf modeChanged multisample traitChanged multisample traitFir doublePreProcesChanged default stand_call_confChanged output file to .gzNew versionMoved all to afterGraph functionFix default mapAdded combineVariants stepFix multiple issuesAdded index as output fileYamsvp pipeline changes, including the Clever as pipeline instead as CommandLine function. Allowing post processing of Clever results and such..Extend the mapping pipeline with the new aligner: StampyFix on correct readgroupFix on bam inputput all back because breaking some gatk modulesfix any2list functionFix interval passingFix on readgroup itemsAdded support for bam files as input for pipelineFix default aligner in constructorMerge branch 'peter' of git.lumc.nl:biopet/biopet into waiyiMock version of Breakdancer mini pipelineDon't keep the chunked fastq files.