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Hi, there:
I got a few theoretical and technical questions, listed below. It would be great if you guys could shed some light.
1. Figure 1 of the paper Sekar’s 2018 paper https://www.nature.c…
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Dear authors and users,
Could you help me with the following?
When doing:
**~/projects/def-rtadros/tools/mtag/mtag.py --sumstats file1.txt,file2.txt,file3.txt --out ./mtag_metaformat --n_min 0.…
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It turned out that the summary statistics generated in `array-combined/gwas/current` does not match the number of expected lines (1,080,969).
A majority of them have 1,080,566 lines indicating that…
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Hi - I am **highly** interested in getting this tool installed on a power9 system. Is there support for that?
Bgen is installed just fine, but we have never been able to install plink (or plink2…
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# GWAS freeze version 2020/8/15
Output dir:
`/oak/stanford/groups/mrivas/ukbb24983/array-combined/gwas/freeze/20200815`
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In #21, there were 302 files that need to be performed.
After finishing #20, this number was reduced to 236.
We submitted those on scg4.
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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 …
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It turned out that the summary statistics generated in `array-combined/gwas/current` does not match the number of expected lines (1,080,969).
There are 880 files with 1059397 lines (meaning that 21…
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As we see in #27, we would love to compute LDSC h2 first.
We submitted jobs in `/oak/stanford/groups/mrivas/users/ytanigaw/repos/rivas-lab/ukbb-tools/04_gwas/extras/finngen_r3`.
```
8_ldsc_h2.s…
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We have a working version of meta-analysis summary statistics. When we finalize the summary statistics from each population, we should refresh the M-A as well.