How to get vcf not from g.vcf?

Question

[woojoy14]

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?

Answer 1

[Pierre Lindenbaum]

I know that g.vcf is including vcf in it but is it possible to get vcf not from g.vcf?

remove -ERC GVCF to get a .vcf from a .bam