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=== Creating Marker-Based Kinship Matrix ===
=== Creating Marker-Based Kinship Matrix ===
Create kinship matrix (IBS or BN, BN is preferred) using emmax-kin. Make sure that both .tped and .tfam file exist with the same prefix. The intel implementation of emmax-kin should be orders of magnitude faster than previous implementation
Create kinship matrix (IBS or BN, BN is preferred) using emmax-kin. Make sure that both .tped and .tfam file exist with the same prefix. The intel implementation of emmax-kin should be orders of magnitude faster than previous implementation
IBS matrix
% emmax-kin-intel64 -v -s -d 10 [tped_prefix] (will generate [tped_prefix].aIBS.kinf)
BN (Balding-Nichols) matrix
% emmax-kin-intel64 -v -d 10 [tped_prefix] (will generate [tped_prefix].aBN.kinf)
=== Run EMMAX Association ===
=== Run EMMAX Association ===
