Hello Everyone,

I am looking for the best way to get linkage information from unphased whole genome population data. I have a vcf file with multiple individuals from different populations. The data is unphased but I would like to detect regions with an excess of linkage disequilibrium as a measure of positive selection. I have not phased the data because I have a limited number of individuals per population of a non-model species and therefore worry that phasing will be very inaccurate.

What do people think would be the best way to detect regions with high levels of linkage disequilibrium? I was thinking something like VCFtools `--geno-r2` option might be suitable.

Thanks for your help!

Best regards,  
Rubal
<p>The --geno-r2 option in vcftools should be enough for your needs; however, you can not calculate linkage disequilibrium if your data is not phased. If you were studying human individuals, I would suggest you to <a href="https://mathgen.stats.ox.ac.uk/impute/impute_v2.html">impute</a> more genotypes by merging it with the 1000 Genomes data, but if you say that you are working with a non-model organism, this is not an option. Is there a close model organism that you can use to impute data?</p>
