Error occured at the PHG imputation step: allele in genotype not in the variant context

Question

[xeod21]

Hi, PHG team.

I am using PHG Docker container (maizegenetics/phg:1.5) to imputate haplotypes from 10 samples. I used the GVCF files as a input to run the PHG and every steps before the imputation (pathToVCF) ended without error. However, i got the error which described below at imputation step, PathsToVCFPlugin.

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Caused by: java.lang.IllegalStateException: Allele in genotype GA not in the variant context [G*, A]

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My VCF output file contains the columns about 10 samples and its genotype but it shows only a few information because PHG was halted. This error occured when i using PHG Docker container (maizegenetics/phg:1.4). Is this error means my GVCF files has some problem?

Here, i attach the Google Drive link contain my PHG commands, config file, VCF output file, and imputation log file for troubleshooting.

https://drive.google.com/drive/folders/15bsc3Z-iZB1O2_BjB7X3pj7STYdGV9wd?usp=sharing

I really need some help to handle this error.

Thanks.

[lcj34]

We are aware of this problem and are trying to diagnose. I will post here when we have a solution and a new build.