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call rate filter #288

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1teaspoon opened this issue May 16, 2024 · 0 comments · Fixed by #305
Closed

call rate filter #288

1teaspoon opened this issue May 16, 2024 · 0 comments · Fixed by #305
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@kliao12

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@1teaspoon
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Currently at call rate filter step the qc pipeline filters low call rate samples first and then filters low call rate loci
We would like to change this process to first filter low call rate loci and then filter low call rate samples.
@kliao12 kliao12 self-assigned this Jun 12, 2024
@kliao12 kliao12 mentioned this issue Jul 1, 2024
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@kliao12 kliao12 linked a pull request Jul 1, 2024 that will close this issue
switch snp and call rate filters #305
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@jaamarks jaamarks mentioned this issue Sep 6, 2024
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jaamarks added a commit that referenced this issue Sep 13, 2024
@jaamarks
Merge pull request #320 from NCI-CGR/issue-288-update-qc-report
3cfb8b3 
report: Clarify loci filter precedence in QC_Report.docx (issue #288)
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@kliao12 kliao12

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switch snp and call rate filters NCI-CGR/GwasQcPipeline
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@kliao12 @1teaspoon