Gwas Analysis Starting Point
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7.3 years ago

Hi there,

Since I am new to GWAS I want to know , how can I start with GWAS analysis with genotype file and SNP info file available with me? Below are the sample data of those two files:

1) genotype file:

1 DVDAC003 0 0 0 0 A G T T A A C G C G A C A C A A C G A G G G C G G G A G C C G G G G G G 0 0 0 0 0 0 0 0 0 0 0

2 DVDAP001 0 0 0 0 A G T T A A G G C G A A C C A G G G A A G G C C G G A G C C A G A G G G 0 0 0 0 0 0 0 0 0 0 0

3 DVDAP003 0 0 0 0 A G T T A A C C G G C C A C G G C G G G A A G G G G A G C C G G A A G G 0 0 0 0 0 0 0 0 0 0 0

4 DVDAP004 0 0 0 0 G G T T A A C G C G A A C C A G C G A G G G G G G G G G C C G G A G G G 0 0 0 0 0 0 0 0 0 0 0

5 DVDAP006 0 0 0 0 G G A T A G C G C G A A C C A G C C A A A G G G G G G C C G G A G G G 0 0 0 0 0 0 0 0 0 0 0 0

2) SNP information:

9 200006 159.0341 139046223

2 200052 218.8627 219783037

2 200053 218.8631 219783289

16 200070 36.22 16174099

16 200078 36.22 16194115

16 200087 36.22 16153665

Though I have experience in GWAS analysis using .ped and .map file in plink, I am not able to get initial trigger to go ahead with this data files. Please provide me assistance in inception of GWAS analysis with these available files.

Thanks,

Mandar

gwas • 2.7k views
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Do you have phenotypic information?

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No, whatever I have, I have pasted above. Is it sufficient information?

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