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Run single variant and aggregation tests only within region #26

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welchr opened this issue Mar 16, 2020 · 1 comment
Open

Run single variant and aggregation tests only within region #26

welchr opened this issue Mar 16, 2020 · 1 comment
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@welchr
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welchr commented Mar 16, 2020

Especially as input files and number of studies gets large, it would be useful if rare metal could use tabix from the results and covariance matrices to select only the parts of the genome it needs for the test instead of loading the entire chromosome/genome. It would make the process less computationally cumbersome or have the benefit of not requiring us to again make many subsets of the initial files for specific analyses that are computationally feasible.

Currently I believe --range chr:start-end works partially for this, though it looks like it may still run the single variant analysis chromosome-wide. Needs further assessment.

Also this parameter appears to be undocumented.

@welchr welchr added this to the 4.16.0 milestone Mar 17, 2020
welchr added a commit that referenced this issue May 9, 2020
This limits both single variant and group test results to only include the range specified by the user

Implements #26
welchr added a commit that referenced this issue May 9, 2020
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welchr commented May 9, 2020

Since docs aren't maintained in this repo, we'll have to edit wiki to include this new "official" parameter.

Usage is: --range chrom:start-end. Single variant tests and group tests are limited to only those within that given range/region.

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