Adding New Samples to Existing VCF Files graphtyper2

Question

[upadhyay.maulik]

I have a question regarding the recommended approach for adding new samples to an existing set of VCF files. I currently have filtered VCFs generated from 629 samples using graphtyper2, and I would like to add 5 additional samples. My current workflow is:

1). Used graphtyper genotype to call variant sites from the 5 new samples.

2). Used --vcf=<sites_629_samples>.vcf.gz to genotype the 5 new samples at the existing variant sites.

3). Then used --vcf=<sites_5_samples>.vcf.gz to genotype the 629 existing samples at the new variant sites found in step 1.

4). Finally, I removed duplicates and merged the resulting VCFs.

Is this the correct approach for updating the existing VCF with additional samples and novel variant sites?

Thank you in advance!