I did variant calling of a bam file (it's related to whole-genome sequencing of a human sample) with GATK (version 4) and then tried to annotate it with dbsnp, but it was not successful. I download human reference genome and dbsnp files from the following addresses:
For annotation with dbsnp, firstly, I used the below command from GATK
Gatk VariantAnnotator –R genom.fa –I file1.bam –V file1.vcf –A coverage –D All_20180418.vcf
Warning: VariantAnnotator is a BETA tool and is not yet ready for use in production
and didn’t return me any output. So, I used bcftools for annotation with the below command:
bcftools annotate –c ID –a All_20180418.vcf.gz file1.vcf.gz > file1_annotate.vcf
But, bcftools also didn’t annotate my vcf file without returning any error.
Could you please help me what’s wrong and kindly tell me how I can annotate my vcf file with dbsnp?