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We convert the UKB sumstats into LDSC munge format.
This will enable us to perform
- GBE global meta-analysis #25
- Compute LDSC intercept as a GWAS QC metric #21
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Hello - I'm just flagging an issue with the coding of the effect / non-effect alleles. In the Wiki, it states that A1 is considered the effect allele. However, whenever I read in data, MTAG uses A2 …
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When running susie_rss, I get an error:
Error in if ((elbo[i + 1] - elbo[i]) < tol) { :
missing value where TRUE/FALSE needed
I only get this error for a small proportion of regions I'm test…
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Hi Phil,
Thanks so much for providing this. It is amazing and has saved me a huge amount of time!
I was wondering if you could please check the ATC code for 1140860802 & 1141180598 in the data…
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In the AMP PD data explorer, when I click on the down arrow or in the search bar itself, a list of facet fields pops up.
These only appear to be for the sample-related tables, not the participants.…
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https://github.com/cpanse/MsBackendRawFileReader/blob/63d90b342cce3552b51ccca73b2adcad1eadc3b6/src/MsBackendRawFileReader.cs#L59
```{r}
#R
# BiocManager::install('cpanse/MsBackendRawFileReade…
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Hi,
I am trying to use the tool on the GTEx and GWAS example data, before using it on mine, but it does not seem to work.
Data used:
UKBB Height as from example, lifted over to hg38 as from exam…
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### What happened?
[reporter's note: IIRC, exit code 137 indicates that the "container" in which the worker JVM was executing exceeded memory limits. It seems likely that whole stage codegen has eith…
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**Description**
The following samples failed library prep, but they do not show as failed, they instead are shown as 'empty wells' from a certain plate onwards in the pipeline.
UKBB_MP8190896
U…
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Now that we've reconfigured and refactored the phasing pipeline to improve SV performance on 10Mbp, we probably need to make additional changes to improve scalability for whole chromosome/genome runs.…