Question: updating vcf file from rsIDs of dbsnp138 to dbsnp144
0
gravatar for waqasnayab
2.7 years ago by
waqasnayab160
Pakistan
waqasnayab160 wrote:

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.

sequencing snp dbsnp gene genome • 1.0k views
ADD COMMENTlink modified 2.7 years ago by trausch1.1k • written 2.7 years ago by waqasnayab160
2
gravatar for trausch
2.7 years ago by
trausch1.1k
Germany
trausch1.1k wrote:
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

 

ADD COMMENTlink written 2.7 years ago by trausch1.1k
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