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This includes gwas catalog + UKBB neale conveniently
https://genetics.opentargets.org/
Fedja updated
4 years ago
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Dear SAIGE developer,
I am currently conducting a binary traits GWAS on UKBB using SAIGE, and I have a couple of questions regarding the step 1 calculation of the full GRM matrix.
Full Genome Da…
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Hey, when trying to install the package, pip cannot resolve the requirement `batch`. Which package is it you require?
https://github.com/Nealelab/ukb_common/blob/c46cac78b9472238b83ef55dccd354c9639…
enryH updated
5 months ago
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Hi,
I've run into an issue with converting UKBiobank summary stats due to the extremely small p-values that I have a crude fix for but was wondering if you guys had already solved in your analyses.
…
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The current seqr sample qc pipeline does not apply hard filters in the `get_qc_mt` function: https://github.com/broadinstitute/gnomad_methods/blob/0b8e1007aacabcb81e4093d9e315ac6f7c92651b/gnomad/sampl…
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This is a behaviour of AFNI's 3dROIMaker that we need to account for. From the 3dROIMaker documentation (https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dROIMaker.html):
> If an INSET ROI has …
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I ran code just to test converting CWL pipeline below:
`java -jar dxCompiler-2.4.7.jar compile /Users/****/****/UKBB/analysis-workflows/definitions/pipelines/CH_exome_Final2.cwl -language CWL -proj…
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After the best ldpred score has been determined, either test the score on validation data (split UKBB data? MVP?) or cross-validation in R
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Hi Authors,
I am trying to reproduce the results of Fig3, I was able to run and finish almost all steps except
```
utils_GWAS.plot_enrichment_per_gene_linked_tiles_peaks([pbmc_ukbb_file], ukbb_f…