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missing samples after CombineGVCFs


I am working on the analysis of 180 exomes, (60 trios). To avoid memory problems, I'm combining the individual gvcf files into 3 cohorts of 20 trios (60 exomes). Then, I genotype the 3 cohorts together. Looking at the final vcf file, there are several samples missing - out of 180 samples, 11 are missing. The samples were excluded during CombineGVCFs. I didn't receive any error message, the samples are just missing from the combined g.vcf files.

I am using GATK 3.5 and Build 37, if that is meaningful.

Is there an obvious reason why this is happening?

Thanks for your help,


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