Error: failed loading target haplotypes

[TheRainInSpain]

Hi, I mmeet an error like below, I have no idea why this happens, I asked ChatGPT and it told me that in this position, it contains both haploid and diploid genotypes, But I checked the target.vcf file and found that in that position, it only contains diploid genotypes. Can anyone help me to solve the issue?

minimac4 -r Chr01 ref.msav target.vcf.gz -o imputed.vcf.gz
minimac v4.1.6

Imputing Chr01:1-1900000 ...
Loading target haplotypes ...
Error: Sample 009 changes ploidy at Chr01:135680
Error: failed loading target haplotypes

Thanks a lot.

[jonathonl]

The error message is saying that sample 009 has a ploidy at position 135680 that is different than that sample's ploidy at the preceding variant.

[TheRainInSpain]

Hi, which preceding variant is related to the ploidy. I did not find that in the help message after run command minimac4 -h

[jonathonl]

You should be looking at the variant immediately preceding the one reported in the error message. A sample needs to have consistent ploidy for the entire region being imputed.

[TheRainInSpain]

Thank you so much and I have solved that issue. But I meet another issue which is :
Error: not enough target variants are available to impute this chunk. The --min-ratio, --chunk, or --region options may need to be altered.
I wonder what caused this issue.

[jonathonl]

The most likely cause is that your array data doesn't have have enough variants present in the chunk being imputed.