Has this tools been removed in the last release ?
It is now in the latest release
I used gatk4 for variant annotation of my vcf file with dbsnp with the below command:
Gatk VariantAnnotator –R genom.fa –I file1.bam –V file1.vcf –A coverage –D All_20180418.vcf
GATK4 said “Warning: VariantAnnotator is a BETA tool and is not yet ready for use in production” and didn’t return me any output. Could you please help me out what's wrong? I'm not sure about the -I flag in my above command, please kindly tell me if it is correct?
--output,-O:File The file to which variants should be written Required.
--variant,-V:String A VCF file containing variants Required.
Please provide an output file. That should solve the problem.
I hope that helps.
When running VariantAnnotator (gatk4 release gatk-22.214.171.124), it still states " Warning: VariantAnnotator is a BETA tool and is not yet ready for use in production". Is there a plan to make VariantAnnotator a production level product soon?
Yes there is and we are working on it!
@bhanuGandham, Is there a timeline for release?
I will check with the developers and get back to you.
Looks like it won't be until next year that this tool is released for production use. For now it is in beta and should be used at your discretion. You can track the progress of this tool here.