Tagged with #dbsnp138
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Created 2016-01-23 13:25:11 | Updated | Tags: snp dbsnp138 dbsnp144 rsids

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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.

Thanks,

Waqas.


Created 2013-12-03 11:22:27 | Updated | Tags: variantstovcf dbsnp138

Comments (1)

I have used the following command $ java -jar GenomeAnalysisTK.jar -T VariantsToVCF -V:OLDDBSNP snp138.txt -R genome.fa -o snp138.vcf to convert human snp138.txt file downloaded from http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ to .vcf format. As output the snp138.vcf file has been generated which has the size as 0 and the other 2 files have been generated as snp138.txt.idx and snp138.vcf.idx. How can i get the snp138.vcf?