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.