After running the 3. Run PTWAS scan - step.
The output (stratified.txt) mentions of n number of SNPs contributing to the association. However, it is not known the SNP detail (rsids) is it possible to derive that information. As I would like to run a coloc (https://chr1swallace.github.io/coloc/articles/a03_enumeration.html) on the expression and phenotype using the beta and variance.
Eg..
CHR POS GENE CLASS SUBCLASS NSNPS STAT PVAL INFO
1 817341-823246 ENSG00000225880.5 eQTL Whole_Blood 1 1.855420 6.3536e-02 OK
Hi,
After running the 3. Run PTWAS scan - step. The output (stratified.txt) mentions of n number of SNPs contributing to the association. However, it is not known the SNP detail (rsids) is it possible to derive that information. As I would like to run a coloc (https://chr1swallace.github.io/coloc/articles/a03_enumeration.html) on the expression and phenotype using the beta and variance.
Eg..
CHR POS GENE CLASS SUBCLASS NSNPS STAT PVAL INFO
1 817341-823246 ENSG00000225880.5 eQTL Whole_Blood 1 1.855420 6.3536e-02 OK
Thanks Murali