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.
Help with GenotypeGVCFs in GATK4
I am trying to run GenotypeGVCFs on a database I just created using GenomicsDBImport. However, I am getting an error I don't know how to fix. The error is:
A USER ERROR has occurred: n is not a recognized option
The script I'm using is here:
singularity exec gatk-4.img \
/opt/gatk/gatk GenotypeGVCFs \
-R $REFERENCE/Gasterosteus_aculeatus_gasAcu1.fasta \
-V gendb://$DATA_DIR/genomicsdb_array \
-G StandardAnnotation -newQual \
I have to use GATK in a singularity image on the cluster I have access to. To me, it's unclear what 'n' is referring to. Also, during the GenomicsDBImport step, I used the line below:
--genomicsdb-workspace-path $path/chr1/DE_M_chr1_DB \
Yet, there is no directory called "DE_M_chr1_DB", instead there is only a directory called genomicsdb_array, and 4 files. Is this correct?
Thanks for your help!