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bgen logistic regression gives wrong results

5

Hi ! when running rvtests --single wald with UK biobank bgen files as input and binary oucomes, I am getting results that differ completely from other GWAS tools that allow...

winkusch

Segmentation fault with condition option

4

Hi, I'm new to RVTest and genetics, so if this is something simple I apologize in advance. I am trying to run a conditional analysis with one SNP as the...

jgmayer67

BGEN file does not work

5

Hi, i converted the UKB chr22 BGEN file to VCF format using PLINK2. I first used PLINK to run association analysis on these two input files to make sure that...

jielab

For gene level models, do they work with rare variants only (i.e., is it required to set --freqUpper 0.05)?

2

1. In the example folder of rvtest package, you did not specify --freqUpper 0.05 in cmd.sh. Here is the example code. If I use --freqUpper 0.05 in the same command,...

ppjeep

Extra column Kinship matrix

7

Dear Xiaowei, for the GIANT/GLC project I have been running all my analysis using rvtest Program version: 20170307. Somehow all of them produce the same log file where an error...

medinacarolina

SnpEff annotated VCF

1

Hello, I have been playing around with the rvtests docker container for a couple of days and things have been running smoothly, thanks for the nice utility! Yesterday I attempted...

Thatguy027

I have encountered a problem when running a recessive analysis with files in the bgen format, I am running the following script, which takes a chromosome, start and end position...

cgrace1978

Allele frequency column does not match N_REF,N_HET,N_ALT column

1

Dear Xiaowei, thank you for developing rvtests. I am using your tool and have realized that from version 20160504 on the allele frequencies reported and the INFORMATIVE_ALT_AC column do not...

sgrosche

Is using setFile slower than geneFile?

3

Sorry, didn't test it thoroughly , but it just "feels" slower, maybe you know the reason? (If not I can create reproducible example.) I tried standard file as input: `--geneFile...

zx8754

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...

gpcr