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I was running FINEMAP and I believe that FINEMAP.check_files() fails to find an existing .cred file
First, I am copying the output of my FINEMAP run:
) ) ) ))))))}}}}}}}} {{{{{{{{{(((((( ( …
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Dear SuSiE team,
I am a huge fan of your method and currently working on a pipeline to use SuSiE, susie_rss specifially, to finemap GWAS regions from UKBB data on binary traits. Although this seems…
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There are a couple of files which I cannot relate to any publicly available file published from the GWAS catalog or the Neale UKBB dataset needed for running the V2D pipeline.
Some files that are …
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In the function SKAT_Optimal_Logistic_VarMatching, there's a call to create a diagonal matrix that is never used. This matrix is never used but the memory allocation can grow quite large.
Line 303…
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In 2022-03 run this ValueError in `baseline_to_condition_occurrence` stops the ETL.
Expected behaviour is that only the transformation fails, but rest of the ETL continues.
```
2022-03-27 08:34:5…
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## 1. Bug description
finemap_loci pipeline fails to find echoverse package?
### Console output
```
Registered S3 method overwritten by 'GGally':
method from
+.gg ggplot2
⠊⠉⠡⣀⣀⠊…
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Examples X998 or X999 in top 25 unmapped Procedures.
- [ ] Look up all administrative codes from the last CDM Inspection Report. Confirm with UCL that these are indeed administrative codes (2)
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Submitting Author Name: Peter Dutey-Magni
Submitting Author Github Handle: @peterdutey
Other Package Authors Github handles: (comma separated, delete if none) @AnikaC-git
Repository: https://g…
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https://github.com/opentargets/genetics-finemapping/blob/master/2_make_manifest.py#L33 references the files `/home/ubuntu/data/genotypes/ukb_v3_downsampled10k_plink/ukb_v3_chr{chrom}.downsampled10k`. …
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In 2022-03 run on real data the baseline_to_condition_occurrence mapping fails. See error message below.
Possible issue could be the array instances, that start at 1 (!) for [field 40002](https://b…