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.

Multiple GVCF inputs for GenotypeGVCFs

jfjfjfjf Member
edited August 2015 in Ask the GATK team


I tried to use GenotypeGVCFs to perform joint genotyping with 5 samples. I used -V mygvcfs.list to submit multiple gvcfs, but I got the following error message:
Invalid command line: No tribble type was provided on the command line and the type of the file could not be determined dynamically. Please add an explicit type tag :NAME listing the correct type from among the supported types.

So, I run again with -V:VCF mygvcfs.list. I got another error:
Your input file has a malformed header: We never saw the required CHROM header line (starting with one #) for the input VCF file

I checked back my gvcfs, the #CHROM header line is present. I also tried to run GeotypeGVCFs by typing the input gvcfs one by one on command line, and it works well.

Any suggestion on why this happened and how can I submit the input gvcfs in list?

I am using GATK version: 3.3.0




Sign In or Register to comment.