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.
Dear GATK team,
I am running the following command:
java -jar GenomeAnalysisTK_v33.jar -R genome.fa -T CombineVariants --variant file1.vcf --variant file2.vcf --variant file3.vcf --variant file4.vcf --variant file5.vcf --variant file6.vcf --variant file7.vcf --variant file8.vcf --variant file9.vcf --variant file10.vcf --minimumN 10 -o combined.vcf -genotypeMergeOptions UNIQUIFY
The output vcf file has the header for the sample columns:
sample.variant sample.variant10 sample.variant2 sample.variant3 sample.variant4 sample.variant5 sample.variant6 sample.variant7 sample.variant8 sample.variant9
What do these numbers represent? For example, does sample.variant10 equal to the 10th VCF file (it would be file10.vcf in this case) and so on?