Question: Download of dbSNP VCF file
1
gravatar for elhlalisoufiane
23 months ago by
elhlalisoufiane10 wrote:

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
ADD COMMENTlink modified 23 months ago by Shicheng Guo8.3k • written 23 months ago by elhlalisoufiane10
1
gravatar for agata88
23 months ago by
agata88800
Poland
agata88800 wrote:

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

Best, Agata

ADD COMMENTlink written 23 months ago by agata88800
1
gravatar for ATpoint
23 months ago by
ATpoint36k
Germany
ATpoint36k 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 COMMENTlink modified 23 months ago • written 23 months ago by ATpoint36k

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 REPLYlink written 23 months ago by dariober11k
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