Latest dbSNP VCF

Question

[MAPK2]

Hi All, I need to annotate a VCF file using dbSNP latest data for GRCh38. I am using annovar to annotate the VCF file. Can someone please guide me to the right location? I was looking at this ftp (https://ftp.ncbi.nih.gov/snp/organisms/) and then went to this: https://ftp.ncbi.nih.gov/snp/organisms/human_9606_b151_GRCh38p7/VCF/

That link has all different VCF files for version 151. I am not sure if this is the latest version (I saw somewhere 155 is the latest version). Can someone please guide me to the right file? Thanks in advance!

Answer 1

[Ram]

This is the directory you're looking for:

https://ftp.ncbi.nih.gov/snp/redesign/latest_release/VCF/

curl -s https://ftp.ncbi.nih.gov/snp/redesign/latest_release/VCF/GCF_000001405.39.gz | zcat | head
##fileformat=VCFv4.2
##fileDate=20210513
##source=dbSNP
##dbSNP_BUILD_ID=155
##reference=GRCh38.p13
##phasing=partial
##INFO=<ID=RS,Number=1,Type=Integer,Description="dbSNP ID (i.e. rs number)">
##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id.  The gene symbol and id are delimited by a colon (:) and each pair is delimited by a vertical bar (|).  Does not include pseudogenes.">
##INFO=<ID=PSEUDOGENEINFO,Number=1,Type=String,Description="Pairs each of pseudogene symbol:gene id.  The pseudogene symbol and id are delimited by a colon (:) and each pair is delimited by a vertical bar (|)">
##INFO=<ID=dbSNPBuildID,Number=1,Type=Integer,Description="First dbSNP Build for RS">

To find this, you needed to either trust the naming (latest_release/VCF) or read the readme: https://ftp.ncbi.nih.gov/snp/00readme.txt

[MAPK2]

Thank you, Ram. I was wondering if these contigs can be replaced by chr1..chrY?

NC_000001.10
NC_000002.11
NC_000003.11
NC_000004.11
NC_000005.9
NC_000006.11
NC_000007.13

[Ram]

bcftools annotate --rename-chrs is your friend.

[MAPK2]

Thank you.