pheweb
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statgen
A tool to build a website to browse hundreds or thousands of GWAS.
How about making a little bit change to support Regenie output? Here is the header of regenie 2.2.2 output ``` CHROM GENPOS ID ALLELE0 ALLELE1 A1FREQ N TEST BETA SE...
The search bar shows only up to ten results. It would be useful to generate a scroll bar list with all the results.
🦑 Hold for final release of LZ 0.14.0 # Purpose The next release of LocusZoom makes breaking changes to how data is retrieved. This PR updates PheWeb to work with...
Hi, Guys: these days, GWAS files have up to 20 million rows, really very inefficient to query and process, if stored simply as a TXT file. I think the VCF...
Phecodes
Hello, Please forgive these naive questions as I am new to PheWAS analysis. For the UK Biobank dataset, I have run a PHESANT (https://github.com/MRCIEU/PHESANT) analysis for a subgroup of individuals...
Regenie have 'inf' in sebeta column which will cause error for Pheweb parse. Maybe we can add one step to remove such records from regenie summary statistics output. ``` pheweb.utils.PheWebError:...
Dear Peter and guys: Previously I mentioend that it is a pity (not necessarily a bug) that Pheweb could not find rsIDs for SNPs simply because their A1/A2 alleles are...
Dear Peter: Please see the error message below. I tried to run "pip3 install pheweb" on a remote server, which has python2 as default (it does have python3 installed). ...
LOG10P: I already have -LOG10P in my summary statistics. Do you think we can make the system compatible to LOG10P ? (summary statistics are from REGENIE 2.2.4) Thanks Shicheng
Dear Peter and guys: 1. I think these days most GWAS don’t have REF and ALT that “must match reference genome” (required by pheweb). Also, I think in the long...