Open pdpalupi opened 2 months ago
You need the following five fields: SNP ID, Ref Base, Alt Base, P-value and Effect Size
However, if you don't have Ref/Alt bases, bridgePRS can figure it out for you, so I don't think this is the problem. Can you send us the command you typed and the log file or the print out that saw on the terminal?
Thanks,
Tade
On Fri, Sep 13, 2024 at 5:20 AM pdpalupi @.***> wrote:
Dear. Clive and Tade
I have 2 sumstats file (1 sumstats from plink and 1 downloaded from GWAS catalog). I tried to run bridgePRS using these two sumstats and it ended
AttributeError: 'Sumstats' object has no attribute 'snp_handle".
My question is : What is the required data in the Sumstat? my header for the downloaded GWAS catalog sumstats are: CHR, BP, SNP, EA, NEA, BETA, SE, P. Thank you so much for your reply.
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The file handle error could be a problem with how bridge uses relative paths to and in the config files, try using absolute paths throughout and let me know. Thanks
On Fri, 13 Sept 2024 at 10:20, pdpalupi @.***> wrote:
Dear. Clive and Tade
I have 2 sumstats file (1 sumstats from plink and 1 downloaded from GWAS catalog). I tried to run bridgePRS using these two sumstats and it ended
AttributeError: 'Sumstats' object has no attribute 'snp_handle".
My question is : What is the required data in the Sumstat? my header for the downloaded GWAS catalog sumstats are: CHR, BP, SNP, EA, NEA, BETA, SE, P. Thank you so much for your reply.
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Dear. Clive and Tade
The problems solved. The absolute paths in my .config files was the problems, Thanks.
Dear. Clive and Tade
I have 2 sumstats file (1 sumstats from plink and 1 downloaded from GWAS catalog). I tried to run bridgePRS using these two sumstats and it ended
AttributeError: 'Sumstats' object has no attribute 'snp_handle".
My question is : What is the required data in the Sumstat? my header for the downloaded GWAS catalog sumstats are: CHR, BP, SNP, EA, NEA, BETA, SE, P. Thank you so much for your reply.