Viewing Plink files in Haploview

Question

[angel0071987]

HI

I am trying to view plink association data files in haploview. I have generated in Plink the .assoc file and have specified in the input files section of haploview (Plink format) the file and the corresponding map file. It does not let me load the data - it comes up with error message of invalid chromosome on line 3151:27. I am not using human data, it is horse data with 31 autosomes.

I want to be able to view the haplotype association files (generated from plink) in haploview - how do I do this? I have tried loading the files into haploview using both the plink format and the Haps Format - neither of which seem to be working...

Any help and advice would be greatly appreciated. Thanks in advance.

[zx8754]

How about divide your file in two chr1-chr22, and chr23-chr31. In second file rename chromosome names to chr1-chr9. So you can view as 2 files separately.

[melaniesmontes]

Did you find a solution? I have the same problem, but I have 4000+ supercontigs, so splitting the file into sets of 22 would be a lot of work! Thanks! Melanie

Answer 1

[Kevin Blighe]

Solution posted here - please try it: A: Manhattan plots and linkage disequilibrium heatmap

That is:

plink --noweb --bfile MyData \
  --chr 5 --from-bp 1000 --to-bp 100000 \
  --snps-only no-DI \
  --recodeHV --out MyData.Haploview ;

Kevin