Hello,

I am running gene based association test (version plinkseq-0.10) for a case- control study of 120 case and 90 control samples (control samples from 1000 genome- population matched). I ran skat using the following command: pseq proj --phenotype phe1 --tests skat --mask loc.group=refseq mac=1-10 >skat.txt

In the output file, the I values for all the genes are represented with a dot. Example:

LOCUS   POS     ALIAS   NVAR    TEST    P       I       DESC

NM_000399       chr10:64571888..64575780        1959,EGR2       13      SKAT    0.0406009    .       0/1(1);0/10(3);0/2(1);0/7(1);0/9(2);1/0(3);3/0(1);8/2(1)

NM_000879       chr5:131877524..131879123       3567,IL5        9       SKAT    0.00085744      .       0/1(1);1/0(6);2/5(1);3/0(1)

NM_001040153    chr13:78273056..78337961        122060,SLAIN1   101     SKAT    0.999999        .       0/1(30);0/10(6);0/2(14);0/3(24);0/4(3);0/5(3);0/6(3);0/7(2);0/8(2);0/9(12);2/4(1);3/0(1)

Does anyone know why the I values are missing? Also in this case, can we trust the P values? Your help is greatly appreciated.

Thanks, Madhu