imputationserver
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genepi
Michigan Imputation Server: A new web-based service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity
Add multithreading to the final data processing step: compressing and encrypting data. The number of threads used at this step will be either 1 (default) or the number specified in...
I'm attempting to replicate the Server's imputation with the 1000G Phase 3 GRCh38 Reference Panel. I started by confirming my local execution of the Eagle pre-phasing matches that of the...
Dear developers, I have this plot. Based on the R2, I don't think I should feel worried but the plot looks very odd. There seems to be some strand ambiguities....
I ran the imputations through the server but now it is a bit unclear what precisely is the difference between `chr9.dose.vcf.gz` and `chr9.empiricalDose.vcf.gz`. Are the latter the allele dosages of...
## Purpose A recent change in minimac 4.1 lead to confusing error messages: jobs were being rejected without an error message, when minimac failed due to allele swaps. The CG...
I am trying to impute Chr X, but I got the message below: ``` Input Validation 23 valid VCF file(s) found. Samples: 780 Chromosomes: 1 10 11 12 13 14...
## Summary TIS has received a small but steady stream of bug reports involving zip file corruption, most commonly when using the AES256 encryption option. EDIT: There are some reports...
Hello, I'm not currently experiencing any problems, I'm just curious how the server QC checks/EAGLE/minimac4 handle multiallelic sites, both in the input data and when imputing genotypes. I've tried looking...
Getting `java.io.IOException: File '...workspace/job-20231206-180508-110/logs/job.txt' not found in workspace.` error while on the disk the file exists in `/home/ubuntu/imputationserver/workspace/job-20231206-180508-110/job.txt`. There is a missed or additional `logs` subfolder. Experiencing error with both...
I am trying to impute though TOPMed web server. However, imputation cannot start because it complains about more than 10000 obvious strand flips. How should I fix this problem with...
