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I've the following queries on running RealignerTargetCreator module in GATK1.4.
1) Is it recommended to provide the target capture BED file to RealignerTargetCreator in case of targeted/exome experiments? Without the bed file, the tool is taking long time (~6-7 hrs). What's the optimal way here?
2) Does running mark duplicates before or after 'RealignerTargetCreator' have any effect on the # of snps/indels? What is recommended?
Look forward to your comments.