Entering edit mode
7 weeks ago
QX
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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/
your link does not even give the description and how them were generated; how can you trust?
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.
thank you!
but do you know what is the 1000GENOMES-phase_3.vcf.gz and can it also be used?
1000 Genomes data is population level survey, you can read about it here: https://www.internationalgenome.org/category/phase-3/