Download of dbSNP VCF file

Question: Download of dbSNP VCF file

23 months ago by

HI everyone ; can someone tell me where to find known indels.vcf and dbsnp.vcf for the GRCh38 reference genome Build thank's

snp • 2.3k views

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modified 23 months ago by Shicheng Guo • 8.3k • written 23 months ago by elhlalisoufiane • 10

23 months ago by

agata88 • 800

Poland

agata88 • 800 wrote:

See here: https://www.ncbi.nlm.nih.gov/variation/docs/human_variation_vcf/

Best, Agata

ADD COMMENT • link written 23 months ago by agata88 • 800

23 months ago by

ATpoint ♦ 36k

Germany

ATpoint ♦ 36k wrote:

dbSNP is the name of the entire database. The VCF files they provide include both SNPs and InDels. For quick retrieval of variantions in certain genomic regions, also download the .tbi (tabix index) and make yourself familiar with the usage of Tabix. I edited the title of your question to make it more clear. Please try to choose more appropriate titles in the future. Cheers!

ADD COMMENT • link modified 23 months ago • written 23 months ago by ATpoint ♦ 36k

To add to yours and Agata's answers (+1), indels can be extracted with bcftools view -v indels mysnps.vcf.gz, see bcftools. (I would resist the temptation of parsing vcf as text using per/python/awk scripts.)

ADD REPLY • link written 23 months ago by dariober ♦ 11k

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