small updates pipelines #639
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…he genotypeCalling pipeline
…te from those in genotypeCalling
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Important: AddOrReplaceReadGroups is changed to overwrite the SortedBam, instead of making a new Bam |
…mediary result that should not be saved, just wastes time calculating
… have qual scores of 83, which should be treated same as those of >= 80
…ality_scores are not options of SplitNTrim in GATK4, so this is not relevant anymore
…coded_quality_scores are not options of SplitNTrim in GATK4, so this is not relevant anymore" This reverts commit 87ce412.
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