Tassel pipeline - LinkageDisequilibriumPlugin

[Vasileia Spyridaki]

Hi guys, 

I am trying to make a linkage disequilibrium analysis. My dataset is very large, so the Tassel GUI version cannot handle it on my laptop. I am trying to use the command line version but cannot correctly form the command. I want to calculate linkage disequilibrium using LD type "Site by All". Could you help me?

I have tried this, but it did not work:

./run_pipeline.pl -Xmx5g -debug -h ./Cultivated_Ca8_Filter_Imp.hmp.txt -LinkageDisequilibriumPlugin -LDType SiteByAll -endPlugin -export ./Ca8.txt

Thank you very much!

Cheers,
Celia

[Terry Casstevens]

I think what you need for SiteByAll is something like this with the
site specified.

./run_pipeline.pl -Xmx5g -debug -h ./Cultivated_Ca8_Filter_Imp.hmp.txt

-ld -ldType SiteByAll -ldTestSite 2 -export ./Ca8.txt

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[Vasileia Spyridaki]

Thank you very much, Terry. It worked!
Cheers.