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A<->T and C<->G lead to shift population shifts in ancestry qc #24

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HannahVMeyer opened this issue May 20, 2020 · 2 comments
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A<->T and C<->G lead to shift population shifts in ancestry qc #24

HannahVMeyer opened this issue May 20, 2020 · 2 comments
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HannahVMeyer commented May 20, 2020 •
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Describe the bug
Data sets with many SNPs of the form A<->T and C<->G may lead to a shift in test population with respect to reference cohort.

Additional context
Would recommend extending plinkQC workflow with removal of A<->T and C<->G SNPs from datasets prior to merging, solves problem.

Kindly pointed out by @e-manduchi.
@HannahVMeyer HannahVMeyer self-assigned this May 20, 2020
@HannahVMeyer HannahVMeyer mentioned this issue May 27, 2020
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HannahVMeyer added a commit that referenced this issue May 27, 2020
@HannahVMeyer
Remove AT, GC SNPS, address #24 and #25
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@HannahVMeyer HannahVMeyer mentioned this issue Jul 7, 2020
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Released on CRAN now

@e-manduchi
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Great, thanks!

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