Download of dbSNP VCF file

Question: Download of dbSNP VCF file

2.6 years 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

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modified 2.6 years ago by Shicheng Guo • 8.5k • written 2.6 years ago by elhlalisoufiane • 10

2.6 years ago by

agata88 • 810

Poland

agata88 • 810 wrote:

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

Best, Agata

ADD COMMENT • link written 2.6 years ago by agata88 • 810

2.6 years ago by

ATpoint ♦ 45k

ATpoint ♦ 45k 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 2.6 years ago • written 2.6 years ago by ATpoint ♦ 45k

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 2.6 years ago by dariober ♦ 11k

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