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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 (https://software.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_variantutils_GenotypeGVCFs.php), the only required input is -V, so why do I get this?

Maybe a possible explanation is the one stated in a similar discussion (http://gatkforums.broadinstitute.org/gatk/discussion/7326/asereacounter-requiring-a-reference), 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


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