Hi friends,
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:
- http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz
- ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/All_20180418.vcf.gz
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
GATK4 said
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?
Many thanks
1 answer
SnpSift Annotate does a good job of annotating the ID field of a VCF. You will have to download the dbSNP VCF, though, which is > 10GB last time that I checked.
I cannot comment on the GATK command because I have never used it. The warning message issue by that command speaks for itself, too.
Regarding BCFtools, you likely have to first unset your VCF IDs with
bcftools annotate --remove ID file1.vcf.gz | \
bcftools annotate -c ID -a All_20180418.vcf.gz file1_annotate.vcf -Ov \
> file1_annotate.vcf
Of course, SnpSift also works.
Nota bene: also check that your contig names are the same as those in the dbSNP VCF. One may have a 'chr' prefix, while, the other, not
Good luck my friend.
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Did you try this one: https://felixfan.github.io/update-SNP-id/