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Hey Sheila, thank you very much for the reply! 1) That's what I was sort of guessing as well, so I'll definitely stick with HC. 2) Maybe I did't mention all the necessary details. So my data is different from the 1000genomes in 2 ways: the exome …
Forgot the link... http://gatkforums.broadinstitute.org/discussion/1259/which-training-sets-arguments-should-i-use-for-running-vqsr It's under "Important notes for exome capture experiments"