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bgen_reader.allele_expectation allocates memory based on the unindexed genotype. This causes problems when indexing a large bgen (for example UKBioBank).
The following code attempts to allocate a …
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Hi Richard,
I've just tried running the phenotype generation script using the examples you provided in the manual and got the following error.
Do you think you could help pointing out where/how…
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This is an estimate of the VM rental time necessary to do the GWAS regressions (similar to https://github.com/related-sciences/ukb-gwas-pipeline-nealelab/issues/8).
Here are current figures:
- T…
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Hi~
Can I get the file "w_hm3.snplist.bz2" from the website(https://alkesgroup.broadinstitute.org/LDSCORE/) ?
I couldn't find it on this website. Maybe, somebody can send me one. Or there is …
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There are many cases where we might want to throw in a few extra samples to match *after* we have inferred a full tree sequence, but without going through the whole inference pathway again. It's also …
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Hi Olivier,
I want to use shapeit4 for a small genomic region phasing (300Kbp). Is there something I should be careful for such task? for example the minimum genome requirement, or parameter setti…
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Dear Kyoko,
I am wondering whether Harmonized GWAS summary statistics is available from GWAS atlas? I want to download some disease specific GWAS statistics from GWAS atlas to follow by MTAG meta-…
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Our download access to https://biobank.ctsu.ox.ac.uk/ is ending on 2021-08-18.. We need to archive as much as possible to our internal servers before that date.
Their download docs are https://biob…
kousu updated
2 years ago
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Dear Xiaowei:
When I use the latest version of rvtest and the BGEN input file, why the log says "Loaded [ 0 ] samples from VCF files"? There is NO VCF file at all. Also, the BGEN file has two par…
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Hello,
I want to use the numpy inspired API to open an bgen using a symbolic link. I want to do this because I don't want to create the .metadata2.mmm file in the shared directory where the bgen li…