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Old 12-09-2011, 02:33 PM   #1
ashkot
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Default VCF SNP Annotation

Hi all, I am relatively new to this area and I wanted some with annotating VCF files. I converted a BAM file from 1KGenomes to VCF and I want to annotate that with dbSNP rsid.

Can someone please help me with the most simple way to annotate the VCF files?

Thanks in advance.

Ashwin
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Old 12-10-2011, 02:16 PM   #2
Heisman
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Not entirely sure what you are asking but if you want the dbSNP rs numbers for a list of SNPs you can run them through a program called ANNOVAR (although that will only query up to dbSNP 132).
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Old 12-12-2011, 10:25 AM   #3
ashkot
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Hi there, what i want is the following. After I have analyzed my data and have a VCF file ready, I want to run that file into some program that will assign the variants an rs id. I looked at ANNOVAR, is there another one that can also accomplish the same?
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Old 12-12-2011, 10:26 AM   #4
Heisman
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You can look into using SeattleSeq: http://snp.gs.washington.edu/SeattleSeqAnnotation/
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Old 07-16-2012, 11:37 AM   #5
krawitz
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www.gene-talk.de can do the annotation for you. all you have to do is uploading your vcf. it is a free annotation, filtering and interpretation tool for human sequence variants.
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