Question: Gwas Analysis Starting Point
0
gravatar for mandar.bobade60
5.9 years ago by
Bangalore
mandar.bobade6080 wrote:

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 • 2.3k views
ADD COMMENTlink modified 5.9 years ago • written 5.9 years ago by mandar.bobade6080
1

Similar question: How to get started learning GWAS analysis

ADD REPLYlink written 5.9 years ago by zx87548.4k

Do you have phenotypic information?

ADD REPLYlink written 5.9 years ago by Philipp Bayer6.5k

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

ADD REPLYlink written 5.9 years ago by mandar.bobade6080
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2151 users visited in the last hour