Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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!!!