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GATK4 Realign around indels

Hi,

Looking through GATK4 best practices for pre-processing fastq files and do not see a "realign around indels" ( in GATK3 : java -jar GenomeAnalysisTK.jar -T RealignerTargetCreator ) . Should I use GATK3 RealignerTargetCreator in my analysis pipeline ? I guess no as it's not in GATK4 anymore ..

Thanks for the great job on GATK4 though !

Answers

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