Finding reference SNP ID numbers from Chrom POS in VCF of my Exome

Question

[pgrovetom]

I'm a novice and have a copy of my own Exome VCF file but it only contains the "Chrom" "Pos" fields but not the "ID" reference SNP ID numbers - they are ".". I'm curious how to use the chromosome position such as "chr5" "7870973" to lookup its associated reference SNP ID numbers such as rs1801394? Preferably automated from a downloadable table. Is there table that contains chromosome position to reference SNP ID numbers that are rare, common and only Clinically relevent?

dbSNP allows a manual lookup of reference SNP ID numbers and shows the chromosome position for GRCh38.P2 and GRCh37.p13 such as:

http://www.ncbi.nlm.nih.gov/projects/SNP/snp_ref.cgi?searchType=adhoc_search&type=rs&rs=rs1801394

When a Exome is sequenced and a VCR file produced, are the "Chrom" "Pos" fields associated with a particular genome version such as GRCh37/38? If so then any reference SNP ID numbers table would need to be associated with the version such as GRCh37 that was used originally to create the VCF file.

I'm looking for an approach for adding the "ID" fields reference SNP ID numbers to my VCF file either manually or automated preferably.

thanks for any advice given I'm a novice learning from the bottom up.

Answer 1

[Pierre Lindenbaum]

Use GATK VariantAnnotator https://software.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_gatk_tools_walkers_annotator_VariantAnnotator.php and the ncbi vcf file of dbsnp ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606/VCF/

Answer 2

[colindaven]

vcfanno is also nice.

See vcfanno

and about VCF IDs: issue