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rocreguant avatar rocreguant commented on June 8, 2024

Hi Shan,
You don't need to make a unique file, you can merge them during running time using hail commands before running VariantSpark (VS).

From your description that's probably going to require a lot of RAM memory, also the more (fast) CPUs the better.

If your cluster allows, it would be most beneficial to run everything at once. By running it all together VS will be able to extract extra information, like cross-chromosome epistatic interactions, that otherwise could not. However, computers have physical limitations so the second best way is to run it chromosome by chromosome and aggregate the analysis.

Another way would be to prune the dataset. You could remove highly correlated mutations using linkage disequilibrium. This way you'd have a "cleaner" dataset. Also, You could use VS on a two-step process. First, each individual chromosome to remove all variants that have no to little importance, and then, run the complete dataset with the variants that passed the importance threshold.

I hope that helps :)

from variantspark.

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