updating vcf file from rsIDs of dbsnp138 to dbsnp144

Question

[waqasnayab]

Hi,

I have a vcf file with ID column (column no. 3) has rsIDs of dbSNP138 build (hg19). Now, I want to update the same vcf file with dbSNP144 build with the same genomic coordinates (hg19). How to that that? In my opinion, it is not the case of liftover as I want to keep the genomic coordinates same but tot update the column 3.

Thanks,

Waqas.

Answer 1

[trausch]

SnpSift can do this:

java -jar SnpSift.jar annotate dbSnp144.vcf variants.vcf > variants_annotated.vcf

This should be the VCF file for build 144:

ftp://ftp.ncbi.nih.gov/snp/organisms/human_9606_b144_GRCh37p13/VCF/00-All.vcf.gz

[rheab1230]

Can you send me dbSNP142.vcf file? I want to annote my .vcf file with dbSNP142.