Jie Huang

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...

test multiple phenotypes in one command line

1

Hi, Can i use something like "--pheno MY-PHENO-FILE --pheno-name pheno1,pheno2,pheno3" to test multiple phenotypes? I could do that in PLINK with the same "--pheno-name" option. Best regards, Jie

BGEN format on UK Biobank data does not work properly

1

Hi, I use RVTESTS latest version to read the UK biobank BGEN file, a command like this: rvtest --inBgen ukb_imp_chr1_v2.bgen --inBgenSample ukb_imp.sample --pheno bmi.pheno.ped --pheno-name bmi --out chr1.rvtest --single score....

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

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,...

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...

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...

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...

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...

Hi, guys: Thank you very much again for your detailed explanation to my previous question on issue #365. Here is my follow-up: 1. I think the “total number of mutations...