Ignore annotations when performing LD score regression

[Melissa Gymrek]

Hello,

I'm new to the Google group so I apologize if this has been answered.

When performing LD score regression, is it possible to ignore some annotation columns in my annot/LD score files? I would like to perform a separate LD score regression for multiple different annotation columns but currently have all of my annotations in a single file.

Thanks,

~Melissa

[Benjamin Neale]

Hi Melissa,

Generally, we encourage people to analyze the annotation in a joint model, rather than serially. The reason being that joint analysis controls for annotations that are in LD with one another and doing a single annotation at a time can be misleading. 

Best,

Ben

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[Melissa Gymrek]

Got it, thanks for the clarification!

~Melissa