java -jar gatk-package-4.x.x.x-local.jar HaplotypeCaller -R ucsc.hg19.fasta -I SRR000982.mapped.sorted.markdup.recal.bam -O SRR000982.g.vcf -ERC GVCF
I've been following the pipeline based on GATK BestPractice and I was told that you don't need to produce GVCF for variant calling. But in this pipeline, it produces rawVariants.vcf from g.vcf.
I know that g.vcf is including vcf in it but is it possible to get vcf not from g.vcf?
If so, how can I get it?