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RealignerTargetCreator and IndelRealigner
The tools RealignerTargetCreator and IndelRealigner are obsolete in GATK4. Are there any replacements for these tools in GATK4?
Also, there are two option -BQSR (used with PrintReads) and -stand_emit_conf (used with HaplotypeCaller) that are not available with GATK4. What should be done in these cases?