rvtests

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1. Could you please add bgen2vcf, bgenFileInfo utitlies into pre-built executable binary package (for Linux 64bit)? 2. In the example folder of rvtest package, you did not specify --freqUpper 0.05...

ppjeep

still negative AF, for binary trait

6

Hi, I just noticed that there are still negative AF value generated by RVTESTS, when my phenotype is a binary trait. Can you please look into this? Best regards, Jie

jielab

LOG message goes to standard error

7

Hi, Xiaowei: When i use "bsub -o my.LOG -e my.ERR" to run RVTESTS, i found that the log message goes to the my.ERR file instead of the my.LOG file. Usually,...

jielab

Segmentation fault when reading BGEN file

6

Dear Xiaowei: When I use the latest version of rvtest and the BGEN input file, why the log says "Loaded [ 0 ] samples from VCF files"? There is NO...

jielab

could not specify multiple phenotypes.

3

Hi, RVTESTS allow "--covar-name cov1,cov2,cov3", but I found that I could not use "--pheno-name trait1,trait2,trait3". It gave me an ERROR : cannot locate phenotype header [trait1,trait2,trai3]. I did see the...

jielab

Dear Xiaowei I have started running chrX analysis using generated kinship and xHemi Kinship. But when I running the command as follow : rvtest-new --inVcf ChrX.combined.reorder.vcf.gz --pheno phenotypes0602.ped --pheno-name men_INV...

zishang30

unbelievable slow speed for --siteFile

4

Please see my comment on #25， it took 43356 seconds to run a regression on 93 SNPs when I used --siteFile. But when i use bcftools first to extract those...

jielab

Empty individual column - very strange!!

3

Hi, Xiaowei: I got the following error for an imputed chunk. I was able to use "bcftools -l" to extract the sample ID columns without any problem. So, exactly what...

jielab

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

gpcr

bed bim fam as inputs

1

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

gpcr