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!!!