Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

m-value is not calculated in meta-analysis by Metasoft #2

Open
tania1304 opened this issue May 8, 2023 · 0 comments
Open

m-value is not calculated in meta-analysis by Metasoft #2

tania1304 opened this issue May 8, 2023 · 0 comments

Comments

@tania1304
Copy link

Hi Developer (@jinghuazhao)

I used Metasoft for GWAS meta-analysis of two traits. The input file of the was based on guidance provided with Metafoft-The plain format of input_file:
Each row is each SNP.
1st column is RSID.
2nd and 3rd column are beta and its standard error for 1st study.
4th and 5th column are beta and its standard error for 2nd study.
6th and 7th column are beta and its standard error for 3rd study.
The flag below flags I used in meta-analysis-

java -jar Metasoft.jar -input merged_data.txt -mvalue -mvalue_method exact -output merged_data_meta.txt

Unfortunately, I see the outfile does not have m-value in M1, M2 column. The M1 and M2 column only contain NC.
Could you please help me on this issue?
I appreciate your time.

Best regards
Tania

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

1 participant