To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at

GenotypeGVCFs not working for 4.beta.3

jjmmiijjmmii Member
edited August 2017 in Ask the GATK team

I am using GATK beta 4.3 (downloaded yesterday) on trio whole-exome data, following best practices on germline SNP/indel calling up to HaplotypeCaller. I was unable to follow the example command in GenotypeGVCFs tool documentation "Perform joint genotyping on a set of GVCFs listed in a text file, one per line":
gatk-launch GenotypeGVCFs -R ~/hg38/Homo_sapiens_assembly38.fasta -V input_gvcfs.list -O trio11.vcf
It exited with this error:

[August 11, 2017 2:27:38 PM HKT] done. Elapsed time: 0.02 minutes.

A USER ERROR has occurred: Cannot read input_gvcfs.list because no suitable codecs found

My input_gvcfs.list looks like this:


I have also tried listing the VCFs one by one, following the example command "Perform joint genotyping on a set of GVCFs enumerated in the command line":
gatk-launch GenotypeGVCFs -R ~/hg38/Homo_sapiens_assembly38.fasta -V F11.g.vcf -V M11.g.vcf -V P11.g.vcf -O trio11.vcf
But it exited with this error:

A USER ERROR has occurred: Argument '[V, variant]' cannot be specified more than once.

Please help! Thank you very much.

Best Answer


Sign In or Register to comment.