hi all
when using RealignerTargetCreator and IndelRealigner of gatk, both of these two programs have --known parameter.
if i want to use reads alignment indel information and known indel information such as dbsnp to do the indel realign, how to use --known parameter for RealignerTargetCreator and IndelRealigner ? use this parameter in both of the programs?
thanks
when using RealignerTargetCreator and IndelRealigner of gatk, both of these two programs have --known parameter.
if i want to use reads alignment indel information and known indel information such as dbsnp to do the indel realign, how to use --known parameter for RealignerTargetCreator and IndelRealigner ? use this parameter in both of the programs?
thanks