Ld Plot Via Haploview

Question

[mandar.bobade60]

I have encountered a problem while loading the locus information file (.hmap) and genotype file (.ped format) onto haploview.

Error in first line in the genotype file

Can anyone help me out?

I've nearly 200,000 markers for analysis, other analysis and graphs of GWAS are coming well but not LD plot.

Below are the initial few lines from from my ped and hmap file:

sample .hmap file: 200052 219783037

200053 219783289

200070 16174099

200078 16194115

200087 16153665

200096 16195546

200124 150564216

200199 40847933

400630 118530141

401327 140007520

401753 32913568

500301 224098852

500556 17350246

500660 86459709

500694 86433796

500710 86420827

ABO_SNP1 135122669

cnvi0000018 171656460

cnvi0000026 172620413

sample of .ped file:

IDAC003 IDAC003 0 0 1 1 G G A A G G A A G G G G G G G A G G A A G G A G G G G G A G A G G G G G G G IDAP001 IDAP001 0 0 1 2 G G A A G G A A G G G G G G G G G G A A G G A A G G G G G G G G G G G G G G IDAP003 IDAP003 0 0 1 2 G G G A G G A A G G A G G G G G G G G A G G G G G G G G G G G G G G G G G G IDAP004 IDAP004 0 0 1 2 G G G A G G A A G G G G G G G A G G A A G G G G G G G G G G G G G G G G G G IDAP006 IDAP006 0 0 1 2 G G A A A G A A G G G G G G G A G G A A G G A G G G G G G G G G G G G G G G

[zx8754]

It is hard to tell without seeing your files .hmap and .ped. Add head http://en.wikipedia.org/wiki/Head_(Unix) of your files to the question

[mandar.bobade60]

I have edited my post and included the initial few lines of .hmap and .ped files.

Answer 1

[lel7lel7]

Check to see both files have the same number of samples (divide2 minus 6 for genotypes) Could do with a head of your file...

[mandar.bobade60]

The number of columns in .ped file is 1661342, i.e. 1661342 - 6 / 2 = 830668 Genotypes.

The number of rows in .hmap files is 830668. So, I think the file numbers is not the problem. But still it is showing problem "Invalid Genotype at line 1".

[lel7lel7]

and is that .hapmap file in format id position (two columns)? Hmm seems OK then. The only other thing i can think to try is making sure you havent put the haploview settings/files in an incorrect order?

I have got this error myself in the past and it was my file format. Sorry I cant be of more help, Best of luck.

[lel7lel7]

Checking my genotype file.... You could try converting to counts...

1 200001697 0 0 1 0 1 1 1 1 2 2 1 2 2 2 1 1

2 200001718 0 0 1 0 1 1 1 1 2 2 2 2 1 2 1 1

3 200004308 0 0 1 0 1 1 2 2 2 2 2 2 1 1 1 1

4 200020986 0 0 1 0 1 1 1 1 2 2 2 2 1 2 1 1

5 201002087 0 0 1 0 1 1 1 1 2 2 2 2 1 2 1 1