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GATKCombineGVCF produced truncated cohort.g.vcf file

I am trying to combine GVCF files from two different samples, run in intervals of 10000000 bases. It worked to get the Haplotypecaller GVCF file. I successfully also combined the two GVCF file in one gvcf file. when I checked it quality I found it covered some part of the interval such as upto first 20000 bases, and getting no information about the remaining bases, while the parent files have complete intervals (1-10000000 bases). Any suggestion please!!!


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