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GWAS finishing effort - Simple line counts check #21
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Update on counts1. Finalized summary statistics files
2. Files that will be fixed with the on-going computation
We are computing the sum stats for those in #19 3. File(s) that need attention
I thought #17 fixed this file, but it was not the case. Also, #20 have some fix. 4. Other incomplete or missing filesThere are 302 files that need to be generated and/or refreshed. For more information, please check here
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#20 is now finished. |
So, in terms of the remaining jobs, we have
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The patch (#19) generated 824 files with 1080278 lines (-691) because the chrY variants were skipped and one file with 1080969 lines.
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Re-computing
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ToDo --> aggregate the |
Aggregate the
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Update on counts
We've already investigated the followings
Unknown error (?)
on-going effort |
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The line count looks good. Based on these results, we started the following computation:
We can now jump on QC: #32 |
As a QC of the GWAS sum stats freeze, we perform line counts.
We identify the list of (pop, GBE_ID) pairs that satisfy the minimum N >= 100 criteria. We then ask whether we have the results in the
array-combined/gwas/current
directory.For the files linked from
array-combined/gwas/current
directory, we applywc -l
to see if the sum stats are complete.Summary
missing sum stats
As of 2020/6/27, we have the following number of traits missing in the
gwas/current
dirThe corresponding analysis notebook.
For others and related, the jobs were submitted.
incomplete sum stats
As of 2020/6/29, here is the summary of
wc -l
across populations.The corresponding analysis notebook.
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