#mismatching-snps

[DM087]

Hi Sam,

I am following your plink PRS tutorial and I have a couple of questions re mismatching-snps section https://choishingwan.github.io/PRS-Tutorial/target/#mismatching-snps .

1. You say in the 'Note' section that 'Most PRS software will perform strand-flipping automatically, thus this step is usually not required.' I am trying to use plink --score and was wondering about running this step. Do you know if plink takes care of strand-flipping when using --score ?
2. Should I be changing anything in the cases where SNP1 in the base data is A/C, and C/A in the target dataset? Do I need to change the .bim file in this case (or the effect allele in base data)?

Thank you for your help.

[choishingwan]

PLINK does not do strand-flipping, though we have a full step-by-step guide on our PRS-Tutorial website (which you are linking to) where we show how to do that with PLINK + R Sam

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On Fri, Nov 19, 2021 at 10:58 AM DM087 ***@***.***> wrote: Hi Sam, I am following your plink PRS tutorial and I have a couple of questions re mismatching-snps section https://choishingwan.github.io/PRS-Tutorial/target/#mismatching-snps <http://url> . 1. You say in the 'Note' section that 'Most PRS software will perform strand-flipping automatically, thus this step is usually not required.' I am trying to use plink --score and was wondering about running this step. Do you know if plink takes care of strand-flipping? 2. Should I be changing anything in the cases where SNP1 in the base data is A/C, and C/A in the target dataset? Do I need to change the .bim file in this case (or the effect allele in base data)? Thank you for your help. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#28>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJTRYX3TE7SGDOJI7C6BWTUMZX3HANCNFSM5IMO3KTA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[DM087]

Thank you for the prompt reply. Much appreciated!
Regarding my 2nd question: what about A/C in base data and C/A in target data? Do I have to change the .bim file or change the effect allele and reverse the sign of beta so that both sets have A/C? How do you deal with it ?

Thank you.

[choishingwan]

It’s shown in the tutorial In short, for PRSice and our trial, we flip the genotype encoding (short of updating the bim)

On Fri, 19 Nov 2021 at 11:47 AM, DM087 ***@***.***> wrote: Thank you for the prompt reply. Much appreciated! Regarding my 2nd question: what about A/C in base data and C/A in target data? Do I have to change the .bim file or change the effect allele and reverse the sign of beta so that both sets have A/C? How do you deal with it ? Thank you. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#28 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJTRYUP6NRPUBXC36GSMSLUMZ5TXANCNFSM5IMO3KTA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

-- Dr Shing Wan Choi Instructor Genetics and Genomic Sciences Icahn School of Medicine, Mount Sinai, NYC

[DM087]

Thanks Sam! Have a nice weekend!

[DM087]

I am still not clear about it. My question is this. Would you reverse the sign of beta given the following

A1 in base GWAS summary statistics file is the same as A2 in target GWAS data?

Thanks

[choishingwan]

It's automated by PRSice

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On Thu, Jul 14, 2022, 6:04 PM DM087 ***@***.***> wrote: I am still not clear about it. My question is this. Would you reverse the sign of beta given the following A1 in base GWAS summary statistics file is the same as A2 in target GWAS data? Thanks — Reply to this email directly, view it on GitHub <#28 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJTRYRW7GMEGBPF5RKRVVDVUCFG7ANCNFSM5IMO3KTA> . You are receiving this because you commented.Message ID: ***@***.***>

[DM087]

Thanks Sam. Sorry, I did not make it clear that I am talking about --score in plink. Does it mean that I will have to reverse the sign of beta in this case? Thanks

[DM087]

@choishingwan any thoughts? thanks

[choishingwan]

Our tutorial has detailed how to do the flip. You can also flip the sign of the summary statistic I think.

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On Mon, Jul 18, 2022, 11:29 AM rs7412 ***@***.***> wrote: @choishingwan <https://github.com/choishingwan> any thoughts? thanks — Reply to this email directly, view it on GitHub <#28 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAJTRYUJGNFOPYBPBFHRQQ3VUVZ47ANCNFSM5IMO3KTA> . You are receiving this because you were mentioned.Message ID: ***@***.***>