Difference between GATK Bundle and Files from Original Sources

Hi GATK Team,

I am Mia Yang. Would like to ask you some questions regarding the resources from GATK bundle.

(1) Is there any differences between the original files (HapMap, 1000G, Mills, etc..) and the one that we can download directly from the GATK bundle? And are these resources compatible with other variant re-calibration tools available out there?

(2) I can see that there are some labelled with hg19 at the back of the file names. Does this means that the files are only compatible with hg19 genome or it is optimized for hg19 and not the others (example hg38 etc..)?

Thank you in advance and have a nice day! =)

Answers

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