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 do I specify a list of samples for GenotypeGVCFs?
This is the recommended code for
java -jar GenomeAnalysisTK.jar \ -T GenotypeGVCFs \ -R reference.fasta \ --variant sample1.g.vcf \ --variant sample2.g.vcf \ -o output.vcf
Is there some way to specify input g.vcfs from a variable or a text file with sample names?
echo "$files" s1.g.vcf s2.g.vcf
cat files.txt s1.g.vcf s2.g.vcf
--variant $files and
--variant <(echo $files), but that doesn't work.