Question: updating vcf file from rsIDs of dbsnp138 to dbsnp144
0
gravatar for waqasnayab
24 months ago by
waqasnayab140
Pakistan
waqasnayab140 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 • 761 views
ADD COMMENTlink modified 24 months ago by trausch830 • written 24 months ago by waqasnayab140
2
gravatar for trausch
24 months ago by
trausch830
Germany
trausch830 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 24 months ago by trausch830
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