Kinship matrix for PLINK ?

[DusanP]

Dear all,

I am very to PLINK and this forum so please excuse possible mistakes. 

I am performing analyses on a family-based study including ~1100 people within ~270 families. The individuals have various types of relationships : Husband-Wife, Parents-Offspring, Grandparents - Grandchildren,... cousins some time.

I know that EPACTS (UNIX only) allows to account for the kinship matrix using command "--kin", but I was wondering whether something similar could be done in PLINK (For Windows). 

GCTA works fine for windows, and allows computing relatedness matrix (--make-grm), based on which, one can calculate PCs summarizing relatedness.

However, I doubt that this is the equivalent of the kinship matrix found in EPACTS...

So, my question is : Is there a way for generating/accounting for the kinship matrix in PLINK?

Thank you for your reply

Dusan

[Christopher Chang]

PLINK 1.9 supports IBS-matrix and GCTA-matrix calculations (--ibs-matrix and --make-grm-bin under https://www.cog-genomics.org/plink/1.9/distance ).  PLINK 2.0 also supports the KING-robust statistic.

Normally the GCTA-matrix is used in mixed model association analysis today, while KING-robust is used when one wants to perform relatedness-based filtering.

[DusanP]

Great, thanks a lot for your reply!