WES vcf file doesn't have any SNP IDs, only position

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9.2 years ago

HumeMarx ▴ 40

Hi

I have a .vcf file generated through GATK (Original vcf run through VariantSelect) hoping to use downstream in Plink for basic association study. However the file seems to contain no SNP IDs. What can I do to get the SNP IDs in to the vcf file? I already have a .fasta reference library.

I have a very basic knowledge of coding.

Whole-Exome-Sequencing VCF PLINK GATK • 2.9k views

ADD COMMENT • link updated 2.2 years ago by Ram 44k • written 9.2 years ago by HumeMarx ▴ 40

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You mean rsIDs right? You can use VariantAnnotator in GATK. You will have to provide dbSNP file along with your vcf file as inout. Alternatively you can try these posts: List Of Dbsnp Rsids And Their Positions SNP rsid by location?. There are many posts on Biostars that can be useful. Search for "assign rSIDs" or "annotate rsIDs".

ADD REPLY • link updated 2.2 years ago by Ram 44k • written 9.2 years ago by Ashutosh Pandey 12k

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Thank you very much. Will try the annotator in GATK.

ADD REPLY • link updated 2.2 years ago by Ram 44k • written 9.2 years ago by HumeMarx ▴ 40

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