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Truth & Control sources- HapMap and 1000G
I apologize in advance if this question seems like a stupid one, but I have always thought that sources such as HapMap and 1000G from the resource bundle that we use in VQSR are comprised of many global samples, but when I peaked inside of the vcfs, I only saw a reference and alternate allele for seemingly 1 sample only. What am I missing here?
If the multisample genotype info is somehow Incorporated into the vcf index file then is there a way to display the contents of the index file so that I can remove all African samples since they are totally irrelevant to my test sample and seem to be negatively affecting The calibration and the calls for my test sample