Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
How to produce output all the variants that are unique in my dataset
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?