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@hsun3163 how the model looks like, and what approximation has been made.
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Dear LCV developers,
We ran three LCV tests to study a relationship between two UKBB traits - varicose (VV, three sets of GWAS data, rg = 0.98 - 1.00) and ostearthritis (OA) - and obtained controve…
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I would like to join the discussion as well.
I was recently developing a new class for storing GWAS summary statistics. I was frustrated to find info and guides scattered all over the place: https://…
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Dear Liu Lab,
Hi~, I'm using EAS eQTL data and I don't have ancestry-matched GWAS data. So I want to use TESLA to conduct TWAS analysis, but I'm not sure about the input of the GWAS data. Here are my…
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We need to be able to determine which is the reference allele.
For example if you have a ref sequence of ATGTGA and at position 3 you have an EA of GT and an OA of G, you have no way of knowing whi…
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Hi, guys:
We could use bcftools to merge multiple regular VCF files with genotype data.
Now, I have multiple GWAS VCF files, each of which have rsID, REF, ALT, BETA, SE, P, etc.
Can I use bcf…
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I fully understand the need for a format with low bioinformatics requirement for data consumers, but sacrificing data integrity (e.g., by separating sumstats and metadata) to achieve that goal seems d…
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I am trying to run `ldsc.py` to measure enrichment of GWAS risk variants in open chromatin regions of interest. I have generated the thinned `*.annot.gz` files for these regions and computed the LD sc…
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gl.plot_miami2(path1=gwas,
path2=exwas,
build="38",
id1="SNPID",
id2="SNPID",
anno1="GENENAME",
…
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Hi,
I have case-control GWAS summary statistics which does not have the N-columns. I tried using the "--use-beta-se" option, but I am getting an error that N was not computed. I guess I still need …