Question: Download of dbSNP VCF file
1
gravatar for elhlalisoufiane
2.6 years 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 • 3.9k views
ADD COMMENTlink modified 2.6 years ago by Shicheng Guo8.5k • written 2.6 years ago by elhlalisoufiane10
1
gravatar for agata88
2.6 years ago by
agata88810
Poland
agata88810 wrote:

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

Best, Agata

ADD COMMENTlink written 2.6 years ago by agata88810
1
gravatar for ATpoint
2.6 years ago by
ATpoint45k
ATpoint45k 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 2.6 years ago • written 2.6 years ago by ATpoint45k

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 2.6 years ago by dariober11k
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