<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40"><head><meta http-equiv=Content-Type content="text/html; charset=us-ascii"><meta name=Generator content="Microsoft Word 12 (filtered medium)"><style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Cambria;
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri","sans-serif";
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]--></head><body lang=EN-US link=blue vlink=purple><div class=WordSection1><p class=MsoNormal>Hello,<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>I am trying to use the palinear software to run GWAS with genotype*covariate interactions and I have family pedigree to account for. I have the software running with the –mmscore function and with the –robust function, but I am not getting the COVAR_SNP_INT variable in my output files. I can get them if I remove the –mmscore function, but that is not helpful, obviously. I am wondering if this a bug in the program or if there is something else I need to do.<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Here is my command line:<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>runon $bin/palinear --pheno $pheno/${trt}1a2_${who}.txt --dose $pheno/doses/$i.mldose.gz --info .temp.$i.mlinfo --interaction=1 --robust --mmscore $pheno/InvVarCov_matrix_${trt}1a2_${who} --out $pheno/MODEL2/$who.$trt.$i > $pheno.$who.$trt.$i.log<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Thank you for any assistance you can provide,<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal>Jennifer<o:p></o:p></p><p class=MsoNormal><o:p> </o:p></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Cambria","serif"'>-- <o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Cambria","serif"'>Jennifer L. Bragg-Gresham, MS<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Cambria","serif"'>Center for Statistical Genetics<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Cambria","serif"'>Department of Biostatistics<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Cambria","serif"'>University of Michigan<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Cambria","serif"'>1415 Washington Heights<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Cambria","serif"'>Ann Arbor, MI 48109-2029<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Cambria","serif"'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Cambria","serif"'>Phone: (734) 763-2161<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Cambria","serif"'>Fax: (734) 615-8322<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Cambria","serif"'><o:p> </o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Cambria","serif"'>Office: 4622 SPH I<o:p></o:p></span></p><p class=MsoNormal><span style='font-size:10.0pt;font-family:"Cambria","serif"'>E-mail: </span><a href="mailto:jennb@umich.edu"><span style='font-size:10.0pt;font-family:"Cambria","serif";color:blue'>jennb@umich.edu</span></a><span style='font-size:10.0pt;font-family:"Cambria","serif"'><o:p></o:p></span></p><p class=MsoNormal><o:p> </o:p></p></div></body></html>