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pdating vcf file from rsIDs of dbsnp138 to dbsnp144

wukhanwukhan PakistanMember

Hi GATK Team,

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 need to update the column 3.

The vcf file is made from the best practices GATK pipeline. Resource bundles available at ftp GATK are used during the pipeline.



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