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4.4 years ago

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

snp • 12k views
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4.4 years ago
agata88 ▴ 850

Best, Agata

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4.4 years ago
ATpoint 66k

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!

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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!

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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.)