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Old 04-07-2011, 07:51 AM   #1
sbaheti
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Default convert snp chip data to VCF format

Hi

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
200006,1104106549,G,G,0.8273,C,C,G,G,B,B,9,139046223,0.8077,1.0000,[A/G],TOP,BOT,,0.983,1.625,0.042,1.583,1144,16950,0.9979,-0.1049,,
200052,1104106549,T,T,0.9487,T,T,A,A,B,B,2,219783037,0.9152,0.8213,[T/A],BOT,TOP,,0.972,0.861,0.037,0.824,1234,10223,0.9905,-0.1911,,
200053,1104106549,A,A,0.6645,T,T,T,T,A,A,2,219783289,0.7133,1.0000,[T/C],BOT,BOT,,0.092,1.630,1.423,0.207,14062,2817,0.0077,0.0185,,


Thanks

Saurabh
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Old 10-25-2011, 12:52 PM   #2
Venkat
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Pls let me know the way...I am looking for the same question..
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Old 03-14-2017, 05:45 PM   #3
Elsie
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A bit late, sorry, but I believe this can be done by converting these files to PLINK format, and then using PLINK/SEQ (https://atgu.mgh.harvard.edu/plinkseq/output.shtml)
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