ld performance in the package

[OmidJa]

Dear Alana,
Hope you are fine.
Actually I just have a question about the ld option in your GBS_SNP_filter package. If two loci are in ld, then both of them will be removed or one of them will be retained?

Thank you for all your supports.

Regards,
Omid

[laninsky]

Hi Omid,

In the detailed workflow we mention that the LD step is used to "chuck out one out of a pair of loci in LD across P populations" (i.e. one of them is retained). Do you think this wording is clear enough? Happy to update it if you think putting it another way would help.

Cheers,

Alana

[OmidJa]

Hi Alana,
Sorry I didn't pay attention to that sentence. It is completely clear to be understood.

Thank you very much.

Cheers,
Omid