same restuls for skat and skat-o tests

[jyle...@gmail.com]

Hi, I'm running skat and skat-o methods using pseq and getting exactly same results for both methods.

Someone can help me with this?

> pseq myproj assoc --phenotype sbp --covar age sex --mask loc.group=refseq --tests skat skato

LOCUS POS ALIAS NVAR TEST P I DESC

NM_001007250    chr1:53489880..53513216 6342,SCP2       8       SKAT    0.0232708       .       0/0(1);11/3(1);8/3(6)

NM_001007250    chr1:53489880..53513216 6342,SCP2       8       SKAT-O  0.0232708       .       RHO=0.999;0/0(1);11/3(1);8/3(6)

NM_001009881    chr1:52900163..53016084 23318,ZCCHC11   11      SKAT    0.833161        .       1/1(1);1/3(1);1/4(1);1/7(1);4/3(1);4/4(1);6/7(4);8/8(1)

NM_001009881    chr1:52900163..53016084 23318,ZCCHC11   11      SKAT-O  0.833161        .       RHO=0;1/1(1);1/3(1);1/4(1);1/7(1);4/3(1);4/4(1);6/7(4);8/8(1)

NM_001004303    chr1:57226803..57271154 199920,C1orf168 5       SKAT    0.193358        .       4/5(1);5/4(1);6/9(1);7/5(1);8/5(1)

NM_001004303    chr1:57226803..57271154 199920,C1orf168 5       SKAT-O  0.193358        .       RHO=0.999;4/5(1);5/4(1);6/9(1);7/5(1);8/5(1)

NM_001004339    chr1:53321443..53359868 440590,ZYG11A   3       SKAT    0.0036213       .       10/3(1);11/5(1);3/0(1)

NM_001004339    chr1:53321443..53359868 440590,ZYG11A   3       SKAT-O  0.0036213       .       RHO=0.999;10/3(1);11/5(1);3/0(1)

Thanks,

Esthers

[xiaof...@gmail.com]

Hi Esthers,

Did you define refseq group by yourself? Could you advise how you did this?

Thank you.

Xiao