Test-drive the GATK tools and Best Practices pipelines on Terra
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Merge gvcf files
I am doing HaplotypeCaller on one of the samples in a trio. In order to increase the analysis speed, I split the variant calling region file into several small ones, which each file contains e.g. 1/8 of the total variant calling regions. Then I did HaplotypeCaller on each small variant calling region file. I got several gVCF files for one sample. The next step is GenotypeGVCFs. Do I need to merge the gVCF files from the same sample before step "GenotypeGVCFs" or can I directly put these gVCF files as the inputs to "GenotypeGVCFs"? If I need to do it before the "GenotypeGVCFs", which tool I need to use?