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-known parameter for RealignerTargetCreator and indelrealign

liuxq_shishuiliuxq_shishui Member
edited July 2012 in Ask the GATK team

Dear GATK scientists,

when using RealignerTargetCreator and IndelRealigner of gatk, both of these two programs have --known parameter.

if i want to use reads alignment indel information combined with 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

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