incongruence result in ABBA-BABA test about angsd HOT 6 CLOSED

I do not know why I cannot make tab in python code here, sorry for that=-=

from angsd.

Hi Yafel

If you use a large block size then each block with correspond to a single scaffold. You can then calculate the D-stat from the .abbababa files. You can see how the abbababa files are parsed in the R/jackKnife.R file.

-Anders

from angsd.

HI Anders,

Thanks so much, actually, I tried to read R script. Sadly, I am not good at R, but I will try my best to look again. If you do not mind, could briefly introduce what's meaning for each of column in abbababa file?
BTW, do you think the large block size will affect the detecting introgression?

Thanks so much,
Yafei

from angsd.

Hi Yafei, Please see the documentation for a description of the output.
http://www.popgen.dk/angsd/index.php/Abbababa#Output

from angsd.

Thanks a lot ^^
Yafei

from angsd.

Ok, Im assuming this can be closed now.

from angsd.