[ensembl-dev] LD : Number of genotypes supported by the program (250) exceeded

[Catherine Leroy]

Thank you very much! :-)

On 23 Feb 2015, at 11:13, Will McLaren <wm2 at ebi.ac.uk> wrote:

> Hi Catherine,
> 
> Yes, you can increase the number by editing and recompiling the C code used to calculate the LD values:
> 
> (/path/to/src/ is where you have the ensembl-variation API module).
> 
> cd /path/to/src/ensembl-variation/C_code
> sed -i.bak "s/#define SIZE 250/#define SIZE 500/" calc_genotypes.c
> make
> 
> You then have to either copy the resultant calc_genotypes file somewhere in your path, or add the path to your PATH environment variable
> 
> export PATH=/path/to/src/ensembl-variation/C_code:${PATH}
> 
> if you use BASH, or
> 
> setenv PATH /path/to/src/ensembl-variation/C_code:${PATH}
> 
> if you use tcsh or csh.
> 
> If you re-run your script it should then use the recompiled binary.
> 
> HTH
> 
> Will McLaren
> Ensembl Variation
> 
> On 23 February 2015 at 10:15, Catherine Leroy <cleroy at ebi.ac.uk> wrote:
> Hello, 
> 
> Me again! Again on LD. 
> 
> I’m still trying to get for : 
> 	snp : rs11010067
> all the LD r2 values. 
> 
> If I use population : 1000GENOMES:phase_1_EUR
> I get the following message : 
> Number of genotypes supported by the program (250) exceeded
> 
> I can work around that using population : 
> 1000GENOMES:phase_1_GBR
> which is a sub population of 1000GENOMES:phase_1_EUR. 
> 
> Is there any way I can increase the 250 limit to be able to use 1000GENOMES:phase_1_EUR? As this would be probably more representative then the sub population?
> 
> Thanks for your help,
> Catherine
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/
> 
> 
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20150223/f7fc5555/attachment.html>