[digitonin]

Gentlemen, there are several issues with VariationHunter.

1) The paths are relative. Its not a compiling issue. Even if you have the location of the binaries in your path, VariationHunter_SC.cpp calls the files in the current directory. What you must do is edit VariationHunter_SC.cpp and change say:

./calProbMinEditRead
to
calProbMinEditRead

2. For the usage of another genome, you will need to make some modifications so that the program knows how many chromosomes there are. This is a tad more complicated so PM me and I'll describe it in detail. Pretty simple to do, but requires some explanation.

Hope this helps.

[hl450]

so anyone found a way to run variation hunter with another reference?

[AIM]

run variationhunter

Can anyone help how to run variationhunter in win or ubuntu?

[feiyang]

Hi Plichel,

I am also trying to use VariationHunter with non-human genome. My output files are also empty. Then I choose to google it because I didn't find more information about this software on their guide or o website. i find this post. So I want to ask for your help if you have already solved this problem.

It seems to change some parameters in running with non-human genome. Is that right? If so, do you mind giving me some guides about it?

Thanks!

[feiyang]

Hi Hl450,

I am also trying to use VariationHunter with non-human genome. But some problems occurred, which I didn't solve. Have you succeed in running the tool with non-human genome. If so, do you mind helping me on how to make it?

Thanks!

[feiyang]

Hi Sponge,

Have you solved the problem? I have the same problems on running VariationHunter with you.

Thanks!