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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.
VariantsToTable for multi-sample VCF's?
Will VariantsToTable work for multi-sample VCF files? I've tried the following command, but it only outputs the column headers:
java -jar ~/tools/GenomeAnalysisTK.jar -R chr1.fa -T VariantsToTable -V cg_100.vcf.gz -F CHROM -F POS -F ID -F REF -F ALT -F F-101-009 -o test.table