Order of samples in family SNV and SV VCFs is different

[sitems]

I am doing trio analysis, and noticed that the order of sample names in call_sv/genome/${FAM}_sv.vcf.gz and call_snv/genome/${FAM}_snv.vcf.gz is different, what causes small problems in my downstream analyses. It would be great if the order was the same.

[jemten]

Thanks for submitting the issue @sitems.
I agree that it would be preferable to have them in the same order and we'll try to fix this in an upcoming release. In the meantime you can reorder the sample columns of your vcf using bcftools view --samples sample1,sample2,sample3 input.vcf