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I hope I have not duplicated the question since I did not find solution.
Suppose I have one variant dataset which just includes variants from ONE sample . If i have another outer datasets (not my test dataset), I can produce variants that are unique in my test call dataset by using --discordance argument like this with no problem:
$ java -Xmx2g -jar GenomeAnalysisTK.jar \ -R ref.fasta \ -T SelectVariants \ --variant myCalls.vcf \ --discordance outerdatasets.vcf \ -o unique_in_my_set.vcf
However, If my sample dataset includes one clinical affected sample and three controls, I want produce all the variants of this affected sample that are unique within this dataset ( discordance of this affected sample comparing with three controls), what tools or commends I can use?