Installing LDSC for newbies

[Ja733]

I'm inexperienced users in bioinformatics but I'm interested in doing LD to estimate the genetic correlation between two traits, and that's why I came here. I have tried to follow the installation information from the GitHub and I downloaded  Anaconda Navigator, but then stock and didn't know what to do next and how exactly I should install LDSC.

Any help with detailed explanations about how to exactly install LDSC and which tools to use will be very appreciated. I have Windows and Mac systems, so any help in either system will be great.

[Raymond Walters]

Hi,

You don't really need to "install" LDSC per se, just download the scripts. 

If you have git installed, then on Mac you should be able to open Terminal (or similar program of your choice), navigate to the directory where you'd like to download LDSC, and then run the command:

 git clone https://github.com/bulik/ldsc.git 

If you don't have git, then you can instead download this file: 

https://github.com/bulik/ldsc/archive/master.zip

and unzip it in the desired directory.

Once you have the code downloaded, you can then invoke ldsc.py and munge_sumstats.py from the command line in Terminal. Tutorials on how to use these scripts are on the github wiki.

I'm not sure we've had anyone try to get LDSC running on Windows. Most of the above should still apply in terms of downloading the code and running it from the command line, but I can't vouch for the specifics.

I should mention that if you're looking to estimate genetic correlation between a set of GWAS results you have and some other GWAS with publicly released summary statistics, then you may alternatively be able to use LD Hub to run your desired analysis. LD Hub will allow you to uploaded your summary statistics file, select which traits you want to estimates genetic correlations with, and then will run the computation and let you download an excel file with the LDSC results.

Cheers,

Raymond

On Apr 11, 2018, at 7:06 AM, Ja733 <jaha...@gmail.com> wrote:

I'm inexperienced users in bioinformatics but I'm interested in doing LD to estimate the genetic correlation between two traits, and that's why I came here. I have tried to follow the installation information from the GitHub and I downloaded  Anaconda Navigator, but then stock and didn't know what to do next and how exactly I should install LDSC.

Any help with detailed explanations about how to exactly install LDSC and which tools to use will be very appreciated. I have Windows and Mac systems, so any help in either system will be great.

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[Ja733]

Thank you so much Raymond, with your help I managed to get this tools working. I followed the tutorials and converted the summary statistics of one GWAS using munge_sumstats.py.

However, I got the following error with the second GWAS summary results. This is almost the same error when I tried to use the LD HUB that is very useful. 

ERROR converting summary statistics:

Traceback (most recent call last):

  File "./munge_sumstats.py", line 602, in munge_sumstats

    'Too many signed sumstat columns. Specify which to ignore with the --ignore flag.')

ValueError: Too many signed sumstat columns. Specify which to ignore with the --ignore flag.

Conversion finished at Thu Apr 12 14:35:28 2018

Total time elapsed: 1.0m:9.06s

Traceback (most recent call last):

  File "./munge_sumstats.py", line 740, in <module>

    munge_sumstats(parser.parse_args(), p=True)

  File "./munge_sumstats.py", line 602, in munge_sumstats

    'Too many signed sumstat columns. Specify which to ignore with the --ignore flag.')

ValueError: Too many signed sumstat columns. Specify which to ignore with the --ignore flag.

Regards,

Jahad

[Ja733]

Resolved, the issue happened because the file has columns for beta, or, and zscore. .. apparently only one is needed 

thanks again

[Raymond Walters]

Hi Jahad,

Great, glad you were able to get it working!

Cheers,

Raymond

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