HaplotypeCaller and GenotypeGVCF
I am performing variant calling on Targetted Exome Samples (TES) (Human) using licensed version of GATK (V2014.3-3.2.2-7-g f9cba99)
My samples are amplicon based targetted sequences.
Currently I perform Haplotype calling for individual TES and then Genotype GVCF step for the samples together. My question is :
1) Is it fine to do Haplotype calling and Genotype GVCF steps for all the TES samples together, rather than doing Haplotype calling for individual samples and Genotype GVCF step for the samples together, as mentioned above.