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/
1 answer
Literally the first result of a Google search
https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0/
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.
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.
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