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Difference between GATK bundle and original data
Dear GATK team,
Good day. I would like to ask about few things regarding the GATK bundle provided at ftp://ftp.broadinstitute.org/bundle/2.8/hg19/.
From the FTP site, there are few variant file (.vcf format) associated with 1000G, Mills, dbSNPs etc. I would like to ask about the differences between them with the original file provided by their original sources. By "hg19", does that meaning all the resource bundles are optimized for hg19 reference genome? How is the files provided at the bundle differs from the original files?
Thank you in advance.