gpcr

installation issue

1

installation : error message: ``` /usr/include/c++/5/backward/binders.h:108:11: note: declared here class binder1st ^ ConjugateGradientSolver.cpp: In function 'int conjugateEigen(const MatrixXf&, const MatrixXf&, double, Eigen::MatrixXf*)': ConjugateGradientSolver.cpp:72:3: error: 'ConjugateGradient' is not a member of...

Optimized SKAT (SKAT-O)

5

Hi Rvtest team, Thanks for creating wonderful tool. I am wondering how to use rvtest for Optimized SKAT (SKAT-O) thanks

bed bim fam as inputs

1

how to use rvtest with .bed .bim .fam files as inputs ? Or I am i missing simple thing?

how to run PCA including all chromosomes at once?

11

how to run PCA including all chromosomes at once? or run separately and sum the eigen values from each chr?

user defined order of traits in multitracks plots

1

Thanks for creating wonder package for plotting GWAS data. I have a quick question: How can we define the order of trait plot in the multitrack plot?

Is GRCh38 /b38/ hg38 supported?

1

Is gemini supports latest 38 human builds yet?

Is there a limit on the number of infofields to print? I was trying to print all the dbnsfp annotated info fields: getting below error ``` Traceback (most recent call...

Enhancement request: I$* to print all INFO fields

1

I$* to print all INFO fields

error with dbNSFP_GERP++ info fields

5

vawk '{print I$dbNSFP_GERP++_RS}' input vcf prints only 0 example line from vcf to test: 11 47353646 . C T . . dbNSFP_GERP++_RS=4.33;dbNSFP_GERP++_RS_rankscore=0.52;dbNSFP_phyloP46way_primate=-0.41;

ExAC Browser RESTful API : connection refused

4

Error in open.connection(con, "rb") : HTTP error 502. Calls: fromJSON ... fromJSON_string -> parseJSON -> parse_con -> open -> open.connection Execution halted Is http://exac.hms.harvard.edu/rest down?