Which known site references should I use for BQSR of WGS/Exome data?
On https://console.cloud.google.com/storage/browser/gcp-public-data--broad-references/hg38/v0, I see a bunch of VCFs:
a) Should I be using all of these for BQSR? If not, how do I choose which ones to use (and when would you want to use the other datasets)
b) The 1000G phase3 dataset is new to me. What's the difference between integrated sites only and v4?
c) What's the Axiom_Exome_Plus data set?
Many thanks for your help.
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