Missing INFO.gz after imputation & Sample ploidy inconsistency error on chrX

[yiiruulin]

I am currently performing imputation on 23 chromosomes in vcf.gz files on my server. However, after imputation, I only obtained .vcf.gz files and did not get INFO.gz like others.

This is the command
minimac4 -t 28 $ref/chr22.msav $vcf/chr22.vcf.gz -o $impute/chr22.dose.vcf.gz --format GT,DS,GP

How can I obtain the INFO.gz file to perform QC based on rsq?

Additionally, when I tried to compress chrX vcf.gz to msav, I encountered the following error message
Error: sample ploidy is not consistent

How can I fix this issue? Thanks!

[jonathonl]

To get a sites-only VCF file, which replaced the info.gz file, you need to specify the output path with --sites chr22.sites.vcf.gz. The INFO fields in the sites-only file are the same as those in the VCF with dosages, so R2 filtering can be done without the sites-only file.

I'm guessing you have PAR and non-PAR regions in the same chrX file and that males in non-PAR are coded as haploid. You should impute these regions separately. Each sample needs to have the sample ploidy for every variant.