This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Error occured at the PHG imputation step: allele in genotype not in the variant context

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.

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

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.

phg imputation practicalhaplotypegraph haplotype
• 1,120 views • link
updated by lcj34 lcj34 • written by xeod21 • xeod21

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

• 0 views • link
written by lcj34 lcj34

0 answers

No answers yet.

Log in to answer this question.

More posts like this