Hi, I have question about how to merge different vcf files as well as separating each sample in the final out put. first i combine 96 samples using java -jar GenomeAnalysisTK.jar \ -T CombineVariants \ -R reference.fasta \ --variant input1.vcf \ --variant input2.vcf \ -o output.vcf \ -genotypeMergeOptions UNIQUIFY then i used annovar for annotation , but at last all variants pooled together and the samples are not separated.
Can i ask how to solve it? Thank you. Parisa