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Recommended -minMAC #148

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jjfarrell opened this issue Aug 9, 2024 · 0 comments
Open

Recommended -minMAC #148

jjfarrell opened this issue Aug 9, 2024 · 0 comments

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@jjfarrell
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Is there a recommended cutoff for the --minMAC parameter for step2 single variant test. The documentation examples use --minMAC=20 but the default is 0.5. We have compared the results to GENESIS and there does appear to be some inflation on the low minMAC <=10 with the SAIGE results.
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@jjfarrell