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Created with Raphaël 2.2.026Sep2217161512111098532129Aug28272625222019181514121187654130Jul29282724232221181514327Jun26232119171312109654327May2621201514Fix bug on executableRemoved samtools viewAdded merge and filterAdded mergeAdded Quality and BAQ optionsAdded filter on HET_REFAdded genotypes to raw vcfMerge branch 'master' of git.lumc.nl:biopet/biopet into waiyiPass filter variants at combine stepFix output dirsAdded merge stepFix bug on missing indexFixe namespacesRun after graph after scriptrecalibration is now optionalSwitch to filtered vcf filesRemove unused linesAdded 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 function