Few questions on RealignerTargetCreator
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.