Problem in manhattan plot

[sarita 693]

I have uploaded data in .txt file and also get Manhattan and qq plot but there is no peak found in GWAS in the plot. There are markers in my data that have reached GWAS significance <10-8 p value . Let me know why plot is not showing any peaks . I am unable to get locus zoom of my top marker. Kindly help me.

[Andrew Boughton]

Thanks for the question.

Have you checked the ingest log file (button on top right of Manhattan plot page)? Sometimes a small number of points can be omitted from the plot if the data is malformed. For example, some gwas programs output pvalues of 0 due to numerical under flow.

If there is a deeper bug let me know and we can investigate further. (A sample would help, Eg a private viewing link sent to me off the public mailing list)

-Andy Boughton

abo...@umich.edu

On Feb 20, 2024, at 3:21 AM, sarita 693 <saritat...@gmail.com> wrote:

I have uploaded data in .txt file and also get Manhattan and qq plot but there is no peak found in GWAS in the plot. There are markers in my data that have reached GWAS significance <10-8 p value . Let me know why plot is not showing any peaks . I am unable to get locus zoom of my top marker. Kindly help me.

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[Azeem Javed]

hi,

have you removed unnecessary tag from pval column, before making plot....

if so, then 

filter out genome wide variants using awk command....

the resultant file have your gw varints

...

if still your plot not appear genomewide variants please let me know...

but share your code

On Tue, Feb 20, 2024, 5:21 PM sarita 693 <saritat...@gmail.com> wrote:

I have uploaded data in .txt file and also get Manhattan and qq plot but there is no peak found in GWAS in the plot. There are markers in my data that have reached GWAS significance <10-8 p value . Let me know why plot is not showing any peaks . I am unable to get locus zoom of my top marker. Kindly help me.

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