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**Problem**
After bridge/intensity normalization of two datasets column MissingFreq is not updated with the new missing frequency.
**Solution**
Recompute missing frequency after normalizign the d…
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I see the library expects the ukb phenotype files as .csv (PHENOTYPE_DATASET_CSV_FILE_PATH). Does the library also support the .tab files (R files)?
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Hello,
I am running LD score regression for the first time and I am completely new in these types of analyses. I have 3 GWASes (EDIC, GOKIND, UKB) where I tested the same binary phenotype (let’s ca…
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This is a broad issue that I'll use to document some of the problems that have come up when scaling out the UKB pipeline.
For convenience, here is a list of issues that have been filed as a result …
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Dear developers,
Thank you very much for developing and mantaining polyfun.
I have been running susieR fine-mapper independently before trying it out within polyfun. The susieR team has a diagn…
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Hi, thanks for the great tool! On UKB WGS data, since concatenating all chunks per chromosome will produce an extremely large bcf, I wonder whether it is feasible to segment the hg38 into 1381 indepen…
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> vcfRT data = gwasvcf_to_TwoSampleMR(vcf = vcfRT, type="exposure")
Error in gwasvcf::vcf_to_granges(.) :
Not all inherits(vcf, c("ExpandedVCF", "CollapsedVCF")) are TRUE.
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Dear Team,
I am wondering How to handle SNPs which are not included in Haplotype Reference Consortium (HRC)? For example, rare/specific SNPs from UKB, FinnGEN, etc.
Thanks.
Shicheng
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@BoPeng we are recently looking into UKB data for some traits we analyze,
https://dnanexus.gitbook.io/uk-biobank-rap/science-corner/guide-to-analyzing-large-sample-sets
the new UKB release is o…
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The 1 million sample HAPNEST dataset (https://github.com/pystatgen/sgkit/discussions/1144#discussioncomment-7654640 ) seems ideal for our purposes.
Larger thank ukb, and no messing with data access p…