PheWeb-UMich

1–14 of 14

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Charlie Repaci, Peter VandeHaar2

Jul 28

Huh, curious. What version of pheweb are you using? What did you set for “hg_build_number“ in config.

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Huh, curious. What version of pheweb are you using? What did you set for “hg_build_number“ in config.

Jul 28

Joseph Chase, Peter VandeHaar2

Jul 28

Specs on what this should take to run?

How many variants? How many phenotypes? I recommend loading on a big machine (50+ cores) or a cluster

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Specs on what this should take to run?

How many variants? How many phenotypes? I recommend loading on a big machine (50+ cores) or a cluster

Jul 28

Charlie Repaci2

Jun 9

Error in QQ plots

I've figured out the issue! My teammate passed me a small subset of the data to work with which

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Error in QQ plots

I've figured out the issue! My teammate passed me a small subset of the data to work with which

Jun 9

Jennifer Huffman, pjvandehaar2

10/3/21

effect allele when creating your own instance of PheWeb

Hi Jenny, PheWeb assumes that all of those are for the alternate allele. Thanks, I just updated the

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effect allele when creating your own instance of PheWeb

Hi Jenny, PheWeb assumes that all of those are for the alternate allele. Thanks, I just updated the

10/3/21

Mokerina Liao, Peter VandeHaar2

8/4/21

how to generate/input phewas data

You need one file for each phenotype (ie, one file per GWAS). Section 3 of the instructions describes

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how to generate/input phewas data

You need one file for each phenotype (ie, one file per GWAS). Section 3 of the instructions describes

8/4/21

Shicheng Guo, Peter VandeHaar2

7/14/21

Github web page

The Manhattan plot pages have a download link. See the top-right of https://pheweb.org/UKB-TOPMed/

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Github web page

The Manhattan plot pages have a download link. See the top-right of https://pheweb.org/UKB-TOPMed/

7/14/21

Shicheng Guo, Sarah Gagliano Taliun2

7/9/21

Pheweb data download - summary statistics

Hi! Thanks for your interest in PheWeb. Below are the locations to download summary statistics for

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Pheweb data download - summary statistics

Hi! Thanks for your interest in PheWeb. Below are the locations to download summary statistics for

7/9/21

Michael Chong, pjvandehaar2

6/19/21

Login Access outside of Google Accounts?

Here are options I can think of: 1. Your users can make google accounts connected to their non-google

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Login Access outside of Google Accounts?

Here are options I can think of: 1. Your users can make google accounts connected to their non-google

6/19/21

James Pirruccello, pjvh2

3/10/21

Effect allele vs minor allele vs non-reference allele in PheWeb

Yeah, it sounds like you figured everything out correctly. You're right that for a variant "

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Effect allele vs minor allele vs non-reference allele in PheWeb

Yeah, it sounds like you figured everything out correctly. You're right that for a variant "

3/10/21

James Warren, Peter VandeHaar4

2/19/21

upper bound on # of phenotypes?

Fantastic - thank you so much! On Friday, February 19, 2021 at 11:09:32 AM UTC-8 pjvh wrote: I added

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upper bound on # of phenotypes?

Fantastic - thank you so much! On Friday, February 19, 2021 at 11:09:32 AM UTC-8 pjvh wrote: I added

2/19/21

Fedik Rahimov, Peter VandeHaar2

2/10/21

R code for PheWEB

I'm glad you like how pheweb's manhattan plots work! Unfortunately, I don't have any

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R code for PheWEB

I'm glad you like how pheweb's manhattan plots work! Unfortunately, I don't have any

2/10/21

Ashley Qin, pjvandehaar2

2/2/21

Speed up "gather-pvalues-for-each-gene"

Sorry about getting back to you so late. Presumably you've figured it out by now. Yeah, that step

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Speed up "gather-pvalues-for-each-gene"

Sorry about getting back to you so late. Presumably you've figured it out by now. Yeah, that step

2/2/21

Pete Santos, Peter VandeHaar2

8/21/20

Having difficult getting started / following the README does not seem to work

It looks like that was failing because there were no significant associations in that tiny test file,

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Having difficult getting started / following the README does not seem to work

It looks like that was failing because there were no significant associations in that tiny test file,

8/21/20

Sarah Gagliano Taliun

8/18/20

Hello. This group is for discussion of PheWeb. GitHub: https://github.com/statgen/pheweb Citation:

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Hello. This group is for discussion of PheWeb. GitHub: https://github.com/statgen/pheweb Citation:

8/18/20

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