Hi,
Lets say I have 20 bams derived form the same targetted sequencing experiment, and I want to push them through the recommended GATK pipleine.
For the RealignerTargetCreator part of realigning around sites of common indels, should I be running it per sample, or can I run it once against one sample and then use the list filethat it generates against all the other bams from the same experiment, on the basis that since the same regions are being sequenced per sample, the same recurrent indel sites will crop up in each sample.
... or have I minunderstood what the intervals.list file that RealignerTargetCreator defines?
Thanks
Lets say I have 20 bams derived form the same targetted sequencing experiment, and I want to push them through the recommended GATK pipleine.
For the RealignerTargetCreator part of realigning around sites of common indels, should I be running it per sample, or can I run it once against one sample and then use the list filethat it generates against all the other bams from the same experiment, on the basis that since the same regions are being sequenced per sample, the same recurrent indel sites will crop up in each sample.
... or have I minunderstood what the intervals.list file that RealignerTargetCreator defines?
Thanks
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