rvtests
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zhanxw
Rare variant test software for next generation sequencing data
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
Hello, I have both MetaScore.assoc.gz and MetaCov.assoc.gz files that are identical to the ones generated by rvtest. Now I want to create their corresponding tbi files that should also be...
I run the following, expecting missing genotypes to be dropped for any given variant: ```raw ./rvtest --inVcf [file] --impute drop --pheno [pheno file] --pheno-name [pheno] \ --sex --covar [pheno file]...
Trying to run burden test on subset of vcf as below: ``` rvtest --inVcf ... \ --noweb \ --pheno ... \ --covar ... \ --rangeList 21:1-11500000 \ #
Similar to plink: `--pfilter [threshold]`. https://www.cog-genomics.org/plink/1.9/assoc > --pfilter causes only associations with p-values no larger than the given threshold to be reported.
There is an extra tab on the header in the output of MadsonBrowning, see example: 
Hi Zhanxw, thank you for your very valuable tool! I have a question regarding the Variable threshold analytic option. In the manual it is stated this option supports both binary...
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....
Dear Xiaowei, Can we do the time to event (Cox regression) GWAS or whole genome/exome study using the RVTest software? Thanks a lot, Aniket
Dear Xiaowei, I was looking at the columns in my rvtest output but somehow the AF (I guess standing for allele frequency) does not match with the report in the...
