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How to Merge the Variants (and other data) if I run the CNVDiscovery & Genotyper in a batch-like way

Dear Genome STRiP users,

I successfully completed the SVCNVDiscovery pipeline in an individual running for the whole 3418 samples and got 29 variants or regions. But when I tried to run the SVCNVDiscovery pipeline in a batch-like way with 100 as the batch size, I got about 10 variants for each batch, and these "10 variants" are different from each batch. Here I have two questions:

  1. How could you merge these variants?
  2. I think after merging, the number of the variants will be less than 10, which is also less than the number of variants found by the individual running, so which strategy is more reasonable: the individual running or the batch-like running?

Besides, I also met the same problem when running the SVGenotyper pipeline -- how can I merge the variants I found in each batch? And there is another problem: to the same batch, for example, to the first batch containing #1 sample to the #100 sample, the variants found by SVGenotyper and SVCNVDiscovery is different. So how can I make these two results be consistent?

Thank you very much.

Best regards,

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