Make a SNP file from the Manifest file #12
Comments
|
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
<#12>, or unsubscribe
<https://github.com/notifications/unsubscribe-auth/ABNG3OFUDDC7C22EWXFZD4LYDIKNNAVCNFSM6AAAAAA7BALGGCVHI2DSMVQWIX3LMV43ASLTON2WKOZRHE4DCMJSGI4DMNY>
.
You are receiving this because you are subscribed to this thread.Message
ID: ***@***.***>
|
|
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? |
|
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?
—
Reply to this email directly, view it on GitHub
<#12 (comment)>, or
unsubscribe
<https://github.com/notifications/unsubscribe-auth/ABNG3OAMA63JF5YF35NJCPLYDJBMBAVCNFSM6AAAAAA7BALGGCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOJYGY3TCNZRHA>
.
You are receiving this because you commented.Message ID:
***@***.***>
|
|
Yeah, you are right, I just used the wrong term here. Really much appreciated! |
|
One last! When combining the datasets, do you recommend to get the intersecting variant (common) for imputation? |
|
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?
—
Reply to this email directly, view it on GitHub
<#12 (comment)>, or
unsubscribe
<https://github.com/notifications/unsubscribe-auth/ABNG3OCM6YEOL4IXOOCUAMDYDJHXJAVCNFSM6AAAAAA7BALGGCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOJYHA3TMMZQGI>
.
You are receiving this because you commented.Message ID:
***@***.***>
|
|
What do you suggest? |
|
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?
—
Reply to this email directly, view it on GitHub
<#12 (comment)>, or
unsubscribe
<https://github.com/notifications/unsubscribe-auth/ABNG3OA5JYU7UKXW5MW7IHLYDJJOXAVCNFSM6AAAAAA7BALGGCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTOOJYHE2DOMZRGY>
.
You are receiving this because you commented.Message ID:
***@***.***>
|
|
Thanks so much for your answers! |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
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.
The text was updated successfully, but these errors were encountered: