adding new samples to already generated vcf files of SNPs

[BioInf2305]

Dear Developer,

First of all, thank you for providing and maintaining this useful tool.

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, 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!

[realgoldace]

I have tried this step by first call variants from 1 new samples, and then I got the novel variants in the new call by using bcftools, and genotyped these variants in the original datasets, then, I genotyping the orginal variants in the new samples, finaly , I merged all these vcf. But I found thant the time to genotyping the novel variants in original dataset takes almost the same time just as genotyping the whole genome, and I try to short the time by introducing regions file, but as the location of the variants is distributed all cross the chromosomes, the bed file of interval length 10000 to cover the novel variants nearly covers the whole chromosomes, if I used some interval more small, more interval used, it will taken more time. Thus, I recommend just use the whole bam set for genotyping, it is simple and easy.