Question

Download of dbSNP VCF file

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5.7 years ago

elhlalisoufiane ▴ 30

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

snp • 20k views

ADD COMMENT • link updated 17 months ago by Brandon • 0 • written 5.7 years ago by elhlalisoufiane ▴ 30

score 3 · Answer 1 · 2018-07-28

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5.7 years ago

agata88 ▴ 870

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

Best, Agata

ADD COMMENT • link 5.7 years ago by agata88 ▴ 870

score 2 · Answer 2 · 2018-07-28

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5.7 years ago

ATpoint 82k

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 5.7 years ago by ATpoint 82k

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So, from the ftp link you provide, which vcf file should be used when using BaseRecalibrator from GATK in order to skip over known polymorphic sites? Looks like 00-All.vcf.gz would be the most thorough, but it is 15 GB. Thanks!

ADD REPLY • link 19 months ago by appropiate ▴ 80

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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 5.7 years ago by dariober 14k