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.
GenomicsDBImport--do multiple samples need individual databases?
I am trying to do variant calling on a reference transcriptome that I've produced, but I have some questions about functionality of GenomicsDBImport, and downstream in SelectVariants. I know that you can only look at one genomic interval per go, but do they all need individual databases?
I've begun running this command from bash, with
$contigs as the list of contigs to go through,
$path gives the absolute path, and
files.txt representing all my samples.
for i in $contigs do gatk GenomicsDBImport \ $(cat files.txt) \ --genomicsdb-workspace-path $path/my_database \ --intervals $i done
I get this error after running it
A USER ERROR has occurred: The workspace you're trying to create already exists. ( /gatk/my_data/my_database ) Writing into an existing workspace can cause data corruption. Please choose an output path that doesn't already exist. Does this mean that I need to create an individual result for each contig? And how does this influence the downstream SelectVariants command?