Hello.
I want to ask how can I combine multiple vcf files into one vcf file
and saving the sample name for each file? how?
because I used before Hail a package and it’s combine to one vcf file but it’s combine also the name of sample to the first file!
I want to do a genotype matrix after that, So I need to put each variants for it’s sample.
Can U help me please 
Unless you have “gVCF” style VCFs this is generally not possible. If you have multiple gVCFs that you want to join, you should investigate GATK’s combine gvcf: https://gatk.broadinstitute.org/hc/en-us/articles/360037053272-CombineGVCFs