Question Regarding GWAS Summary Filtering

[ShanshanHe-44]

Hi Maya,

I hope you’re doing well!

I was wondering about the filtering process you used for the GWAS summary data from UKBB. I prepared the GWAS variants from the Finucane lab and lifted them over to hg38 and keep SuSie only. However, I noticed that the number of traits differs from your dataset after run the pipeline.

Additionally, I see extra columns in your data, such as PP and CredibleSet, which were not explicitly mentioned in your manuscript.

Could you clarify if any additional filtering steps were applied?

Best,
Shanshan

[mayasheth]

Hi Shanshan, I have attached the log file and Rscripts used to process the GWAS variant data-- also required is "CredibleSetTools.R" which is available on GitHub here: https://github.com/EngreitzLab/ABC-GWAS-Paper/blob/main/ABC-Max/src/CredibleSetTools.R. Perhaps the difference comes from removing the coding variants? Hope this helps, ~Maya Sheth

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On Wed, Feb 12, 2025 at 9:43 AM Shanshan He ***@***.***> wrote: Hi Maya, I hope you’re doing well! I was wondering about the filtering process you used for the GWAS summary data from UKBB. I prepared the GWAS variants from the Finucane lab and lifted them over to hg38 and keep SuSie only. However, I noticed that the number of traits differs from your dataset after run the pipeline. Additionally, I see extra columns in your data, such as PP and CredibleSet, which were not explicitly mentioned in your manuscript. Could you clarify if any additional filtering steps were applied? Screenshot.2025-02-12.at.18.41.33.png (view on web) <https://github.com/user-attachments/assets/aa7ae2a0-c8fa-4424-be3f-80dfa822e3fa> Best, Shanshan — Reply to this email directly, view it on GitHub <#9>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKMOFR2EQLWLK3OBDYICW3T2POB5HAVCNFSM6AAAAABXAGYLLWVHI2DSMVQWIX3LMV43ASLTON2WKOZSHA2DQOJVGUYTMMI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***> [image: ShanshanHe-44]*ShanshanHe-44* created an issue (EngreitzLab/GWAS_E2G_benchmarking#9) <#9> Hi Maya, I hope you’re doing well! I was wondering about the filtering process you used for the GWAS summary data from UKBB. I prepared the GWAS variants from the Finucane lab and lifted them over to hg38 and keep SuSie only. However, I noticed that the number of traits differs from your dataset after run the pipeline. Additionally, I see extra columns in your data, such as PP and CredibleSet, which were not explicitly mentioned in your manuscript. Could you clarify if any additional filtering steps were applied? Screenshot.2025-02-12.at.18.41.33.png (view on web) <https://github.com/user-attachments/assets/aa7ae2a0-c8fa-4424-be3f-80dfa822e3fa> Best, Shanshan — Reply to this email directly, view it on GitHub <#9>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AKMOFR2EQLWLK3OBDYICW3T2POB5HAVCNFSM6AAAAABXAGYLLWVHI2DSMVQWIX3LMV43ASLTON2WKOZSHA2DQOJVGUYTMMI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[ShanshanHe-44]

Hi Shanshan,

I have attached the log file and Rscripts used to process the GWAS variant
data-- also required is "CredibleSetTools.R" which is available on GitHub
here:
https://github.com/EngreitzLab/ABC-GWAS-Paper/blob/main/ABC-Max/src/CredibleSetTools.R.
Perhaps the difference comes from removing the coding variants?

Hope this helps,

~Maya Sheth
…

Thank you for sharing! However, I didn’t receive the R script and log file as attachments. Could you please resend them:)

Best,
Shanshan

[mayasheth]

Here is a Google Drive folder with the scripts, let me know if you still have trouble accessing them! https://drive.google.com/drive/folders/1ieLoyKlfkUIlj_y5vc5t0sNbaBUXzU4i?usp=sharing ~Maya Sheth

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On Thu, Feb 13, 2025 at 7:12 AM Maya Sheth ***@***.***> wrote: Sorry about that, did these come through correctly? ~Maya Sheth On Thu, Feb 13, 2025 at 3:44 AM Shanshan He ***@***.***> wrote: > Hi Shanshan, > > I have attached the log file and Rscripts used to process the GWAS variant > data-- also required is "CredibleSetTools.R" which is available on GitHub > here: > > https://github.com/EngreitzLab/ABC-GWAS-Paper/blob/main/ABC-Max/src/CredibleSetTools.R > . > Perhaps the difference comes from removing the coding variants? > > Hope this helps, > > ~Maya Sheth > … <#m_-3764730022175704961_m_-1297674132220271601_> > > Thank you for sharing! However, I didn’t receive the R script and log > file as attachments. Could you please resend them:) > > Best, > Shanshan > > — > Reply to this email directly, view it on GitHub > <#9 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AKMOFR2RJCCLX4S5TJFTDNT2PSAR5AVCNFSM6AAAAABXAGYLLWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNJWGM2DKNJRGM> > . > You are receiving this because you commented.Message ID: > ***@***.***> > [image: ShanshanHe-44]*ShanshanHe-44* left a comment > (EngreitzLab/GWAS_E2G_benchmarking#9) > <#9 (comment)> > > Hi Shanshan, > > I have attached the log file and Rscripts used to process the GWAS variant > data-- also required is "CredibleSetTools.R" which is available on GitHub > here: > > https://github.com/EngreitzLab/ABC-GWAS-Paper/blob/main/ABC-Max/src/CredibleSetTools.R > . > Perhaps the difference comes from removing the coding variants? > > Hope this helps, > > ~Maya Sheth > … <#m_-3764730022175704961_m_-1297674132220271601_> > > Thank you for sharing! However, I didn’t receive the R script and log > file as attachments. Could you please resend them:) > > Best, > Shanshan > > — > Reply to this email directly, view it on GitHub > <#9 (comment)>, > or unsubscribe > <https://github.com/notifications/unsubscribe-auth/AKMOFR2RJCCLX4S5TJFTDNT2PSAR5AVCNFSM6AAAAABXAGYLLWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDMNJWGM2DKNJRGM> > . > You are receiving this because you commented.Message ID: > ***@***.***> >