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genepi / imputationserver

Michigan Imputation Server: A new web-based service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity
https://imputationserver.sph.umich.edu/
GNU Affero General Public License v3.0
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Calculating QC Statistics failed. #103

Open alkaZeltser opened 1 year ago

alkaZeltser commented 1 year ago

Hello, I am attempting to submit to the TopMed imputation server. The server successfully completes input validation (detects all 23 chromosomes and counts all the SNPs) but fails to complete QC statistics calculation with the following error:

Calculating QC Statistics failed.

This message is unfortunately not particularly informative. Is there a way to get more information about what is going wrong?

Thank you!

alkaZeltser commented 1 year ago

Update: the error seemed to be linked to chrX (only ocurring when chrX was submitted). The error mysteriously resolved when reformatting the chrX submission vcf to v4.2. All other chromosomes ran fine with v4.3

mantle-2014 commented 1 month ago

There are special regions known as PAR (pseudoautosomal regions) on the X chromosome. Perhaps this is what makes it unique, as different versions may handle these regions differently