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missing calls from VCF

1. I combined gVCFs of ~100 individuals. However, when I open the file there are missing genotypes. i.e.- not all rows have equal number of genotypes (see attached). I am using GATK_3.4.6 and the command I am using to merge the gVCFs is:
$cmd = "java -Xmx4g -jar $GATKdir/GenomeAnalysisTK.jar -T GenotypeGVCFs -R $genome --dbsnp $ResourcesDir/dbsnp_138.b37.vcf $filesToJoin -o example.vcf";

Where $filesToJoin is a string with -V individual.gvcf

  1. The total number of individuals is 400, and I combined every 100 together. Can I do the calibration with several -input arguments or must I merge all merged files into one?


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