If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

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.

Error with GenomicsDBImport input file


I am trying to run GenomicsDBImport to test my pipeline with just 2 samples. I am using the following code:

gatk GenomicsDBImport \
-V $SCRATCH/active/memtest2/ SRR112728.raw.snps.indels.g.vcf \
-V $SCRATCH/active/secondex/SRR112730.raw.snps.indels.g.vcf \
--genomicsdb-workspace-path $SCRATCH/active/secondex \
-L 20

I get the error:

A USER ERROR has occurred: Invalid argument 'SRR112728.raw.snps.indels.g.vcf'.

I'm not sure what the problem is with this input file. This is in the format specified in haplotype caller documentation. Can you please advise?


Best Answer


Sign In or Register to comment.