I have results from an HRC v1.1 imputed dataset. When using the results (passing the pruned top hits) to DEPICT I get information that the marker is not found in the genotyped data. I assume this is due to the HRC markers not being in the 1000G reference. Question is if HRC imputed data will be supported, and if not, how would I go about updating the reference data?
I did try to look into the background data but the 1000G markers seems tightly integrated with the rest of the reference data so I am not sure how to do this.
I have results from an HRC v1.1 imputed dataset. When using the results (passing the pruned top hits) to DEPICT I get information that the marker is not found in the genotyped data. I assume this is due to the HRC markers not being in the 1000G reference. Question is if HRC imputed data will be supported, and if not, how would I go about updating the reference data?
I did try to look into the background data but the 1000G markers seems tightly integrated with the rest of the reference data so I am not sure how to do this.
Any help would be greatly appreciated!