Make a SNP file from the Manifest file

[abedkurdi]

Hello there,

I would like to ask if it is possible to make a SNP file from the manifest file. I would like to know also if it is possible to use the manifest file with convert_bim_allele.pl.

I am trying to find a way to fix the alternative alleles that are not observed (missing ALT allele) using --fillzero.

I really appreciate you input here!

Thank you.

[kaichop]

In principle it is possible but you have to write a script to do this yourself. Otherwise, just load a genomestudio project (which includes the manifest) and get the allele conversion table from there.

On Tue, Nov 7, 2023 at 6:19 AM Abdullah El Kurdi @.***> wrote:

Hello there,

I would like to ask if it is possible to make a SNP file from the manifest file. I would like to know also if it is possible to use the manifest file with convert_bim_allele.pl.

I am trying to find a way to fix the alternative alleles that are not observed (missing ALT allele) using --fillzero.

I really appreciate you input here!

Thank you.

— Reply to this email directly, view it on GitHub https://github.com/WGLab/GenGen/issues/12, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OFUDDC7C22EWXFZD4LYDIKNNAVCNFSM6AAAAAA7BALGGCVHI2DSMVQWIX3LMV43ASLTON2WKOZRHE4DCMJSGI4DMNY . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[abedkurdi]

Thank you for your prompt response! I have another question, I don't know if you have any idea: Do you why we might get a high number of no-observed alleles? Is it related to the quality of sequencing or what?

[kaichop]

it is a SNP array, not sequencing. If you have high missing rate, it is a genotype clustering issue.

On Tue, Nov 7, 2023 at 9:35 AM Abdullah El Kurdi @.***> wrote:

Thank you for your prompt response! I have another question, I don't know if you have any idea: Do you why we might get a high number of no-observed alleles? Is it related to the quality of sequencing or what?

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[abedkurdi]

Yeah, you are right, I just used the wrong term here.

Really much appreciated!

[abedkurdi]

One last! When combining the datasets, do you recommend to get the intersecting variant (common) for imputation?

[kaichop]

no

On Tue, Nov 7, 2023 at 10:29 AM Abdullah El Kurdi @.***> wrote:

One last! When combining the datasets, do you recommend to get the intersecting variant (common) for imputation?

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[abedkurdi]

What do you suggest?

[kaichop]

I do not understand your question. If your two platforms differ then perhaps only 1% of the markers will remain if you only take intersection, then how can you impute from it? Please check existing literature and guidance on how to do imputation, it is not something that gengen does and not relevant here.

On Tue, Nov 7, 2023 at 10:44 AM Abdullah El Kurdi @.***> wrote:

What do you suggest?

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[abedkurdi]

Thanks so much for your answers!