Question: A strange problem with annotation of vcf file
0
gravatar for seta
22 months ago by
seta1.3k
Sweden
seta1.3k wrote:

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:

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

ADD COMMENTlink modified 18 months ago by zx87549.3k • written 22 months ago by seta1.3k

Did you try this one: https://felixfan.github.io/update-SNP-id/

ADD REPLYlink written 10 months ago by Shicheng Guo8.2k
2
gravatar for Kevin Blighe
22 months ago by
Kevin Blighe61k
Kevin Blighe61k wrote:

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.

ADD COMMENTlink written 22 months ago by Kevin Blighe61k

Yes, I downloaded dbsnp vcf file with 15.2 GB in gzip. Could you please tell me what is wrong in my work to annotate the vcf file?

ADD REPLYlink written 22 months ago by seta1.3k
1

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

ADD REPLYlink modified 22 months ago • written 22 months ago by Kevin Blighe61k

Many thanks for your points. I'll try them

ADD REPLYlink modified 22 months ago • written 22 months ago by seta1.3k

Good luck my friend.

ADD REPLYlink written 22 months ago by Kevin Blighe61k
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