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genepi / imputationserver-docker

Docker Image for Michigan Imputation Server
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ChrX error #9

Open o147942 opened 4 years ago

o147942 commented 4 years ago

I've downloaded the chr X or 1000g reference again because there is no chrX in the folder downloaded from https://imputationserver.sph.umich.edu/static/downloads/releases/1000genomes-phase3-2.0.0.zip. Nevertheless, I found some issues for imputation of chrX using docker image of Michigan Imutation Server.

  1. The sever cannot find reference information of chrX. [ERROR] Minimac reference panel cloudgene/apps/1000g-phase-3-v5@2.0.0/2.0.0/m3vcfs/X.nonPAR.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz not found. Job chr_X.nonPAR (null) failed.

  2. Wrong matching between my dataset and reference for chrX I've already checked my data using 1000 genome reference before imputation (https://www.well.ox.ac.uk/~wrayner/tools/). I uploaded QCed input files. I used "EAS" population and selected the same population of 1000 genome data for the imputation. However, the qcreport reported wrong information. Most of mismatched frequencies were for chrX. I think the server did not use the chrX of EAS population. I checked the frequencies of the variants reported in the qcreport, but the frequences were not those of EAS population.

I attached my qcreport and log files from the docker server. Please check them.

errors.zip