The Frontline Support team will be offline February 18 for President's Day but will be back February 19th. Thank you for your patience as we get to all of your questions!
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?