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GenomicsDBImport / CreateSomaticPanelOfNormals interval list

Good afternoon

I am using the latest version of GATK and trying to prepare PanelOfNormals as described at

and I see that it changed from 4.0 version.

Step 1 worked just fine, but step 2 complains that "A large number of intervals were specified. Using more than 100 intervals in a single import is not recommended and can cause performance to suffer."

Could you please tell me which intervals to use? I always use the same interval list which was used to capture targets for the library prep.

Indeed, the process taking very long time now, whereas for older version it took a few minutes

Thank you


Best Answer


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