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

[Will McLaren]

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
>
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