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Old 04-07-2011, 08:51 AM   #1
Location: Rochester

Join Date: Jul 2010
Posts: 12
Default convert snp chip data to VCF format


I have HumanOmni1-Quad_v1 SNP chip data, do anybody know how can i convert this data into VCF format which can be used as a reference for GATK inplace of dbSNP reference vcf file.
The data looks like

SNP Name,Sample ID,Allele1 - Top,Allele2 - Top,GC Score,Allele1 - Forward,Allele2 - Forward,Allele1 - Design,Allele2 - Design,Allele1 - AB,Allele2 - AB,Chr,Position,GT Score,Cluster Sep,SNP,ILMN Strand,Customer Strand,Top Genomic Sequence,Theta,R,X,Y,X Raw,Y Raw,B Allele Freq,Log R Ratio,CNV Value,CNV Confidence


sbaheti is offline   Reply With Quote
Old 10-25-2011, 01:52 PM   #2
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Location: Canada

Join Date: Jan 2011
Posts: 9

Pls let me know the way...I am looking for the same question..
Venkat is offline   Reply With Quote
Old 03-14-2017, 06:45 PM   #3
Location: Australia

Join Date: Mar 2011
Posts: 85

A bit late, sorry, but I believe this can be done by converting these files to PLINK format, and then using PLINK/SEQ (
Elsie is offline   Reply With Quote

gatk, vcf

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