Hi!
Thanks for creating this pipeline. We are going to use it for Alzheimer's disease research, but our Chromosome 19 fails the HapMap3 overlap test with:
Error: Less than 70% of reference variants are present in the target.
We have verified our target file contains valid, imputed, rsID variants for Chromosome 19, but have been unable to acquire more.
Two questions:
-
Is there a way to change this requirement (e.g., to 65%) in the config files, or do I have to modify a hardcoded script?
-
Will lowering the threshold to 65% cause issues for the final PRS calculations?
Best regards
Peter
Hi!
Thanks for creating this pipeline. We are going to use it for Alzheimer's disease research, but our Chromosome 19 fails the HapMap3 overlap test with:
Error: Less than 70% of reference variants are present in the target.We have verified our target file contains valid, imputed, rsID variants for Chromosome 19, but have been unable to acquire more.
Two questions:
Is there a way to change this requirement (e.g., to 65%) in the config files, or do I have to modify a hardcoded script?
Will lowering the threshold to 65% cause issues for the final PRS calculations?
Best regards
Peter