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How to get vcf not from g.vcf?
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?

vcf gvcf

1 answer

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

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