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 requires a reference

Hi all,
I am trying to do joint genotyping from .gvcf files produced separately per sample, through the command line

java -Xmx4g -jar /bio/GenomeAnalysisTK.jar -T GenotypeGVCFs -V CILtrial/CILsamples.gvcf.list -o CILtrial/CILsamples.gvcf

where CILsamples.gvcf.list is a list of 19 .gvcf files as follows

However, I get the following error message "Walker requires a reference but none was provided."
Based on the GenotypeGVCFs command page (, the only required input is -V, so why do I get this?

Maybe a possible explanation is the one stated in a similar discussion (, i.e. that GATK tools always require a reference..but wouldn't this be discordant with what is stated in the GenotypeGVCFs page?

It may probably be a stupid question,
but I did not manage to find any other plausible answer in the forum.

(version 3.5-0-g36282e4)

Best Answer


Sign In or Register to comment.