input for gatk VariantAnnotator --dbsnp

Question

[QX]

Hi all, I am run:

gatk VariantAnnotator \
       -R reference.fasta \
       -I input.bam \
       -V input.vcf \
       -o output.vcf \
       --dbsnp dbsnp.vcf

I would like to ask where can I find the dbsnp.vcf files. is that the 1000GENOMES-phase_3.vcf.gz? or the vcf from https://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/

Answer 1

[Shred]

Literally the first result of a Google search

https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0/

[QX]

your link does not even give the description and how them were generated; how can you trust?

[GenoMax]

That link comes from GATK help article here: https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle

It is the resource bundle provided by Broad Institute.

[QX]

thank you!

[QX]

but do you know what is the 1000GENOMES-phase_3.vcf.gz and can it also be used?

[GenoMax]

1000 Genomes data is population level survey, you can read about it here: https://www.internationalgenome.org/category/phase-3/

The goal of the 1000 Genomes Project was to find common genetic variants with frequencies of at least 1% in the populations studied.