Question: How to get vcf not from g.vcf?
0
gravatar for woojoy14
10 months ago by
woojoy140
woojoy140 wrote:
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?

gvcf vcf • 251 views
ADD COMMENTlink modified 10 months ago by Pierre Lindenbaum128k • written 10 months ago by woojoy140
1
gravatar for Pierre Lindenbaum
10 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum128k wrote:

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

ADD COMMENTlink written 10 months ago by Pierre Lindenbaum128k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1268 users visited in the last hour