rvtests
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zhanxw
Rare variant test software for next generation sequencing data
Dear Zhan, I am runing a single variant analysis so my command: ../executable/rvtest --pheno pheno --inVcf example.vcf --single wald --out out1 And this command does not output does not report...
Hi zhanxw, Thank you for developing and maintaining RVTests. When I use RVTests v1.9.9-29 downloaded July 29, 2016 with the '--kernel SKATO' option and a relatively large dataset insists of...
Hi, Thank you for the very useful tool, I was wondering if it is possible to add the permutation based P value generation for the burden tests as well in...
Good afternoon, i am getting a "no variants found in gene" output. Does rvtests pick up heterozygous variants? I am interested in those. I have manually checked the data and...
Hi I have run rvtest several times for single variant and grouped tests, and am now trying to use the --meta score,cov for 3 populations of my cohort separately (Afr,...
When both these options are used in the rvtest command --peopleExcludeID and --freqUpper , Does rvtest first exclude the samples listed, and then calculate the new allele frequency at sites,...
I am getting a lot of NAs when running single test rvtest using score method. I can understand that for rare variation the association will fail but I also have...
Hello, This issue has been brough up a few times, but has yet to been resolved. There is not documentation on the definitions of the output except for meta-analyses.
is there a way to include the MAC or MAF in the output for SKAT/SKAT-O results?
Input: genelist=" " # loop over all genes for i in {1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,19,20,22,X}; do run_rvtest_wes="wget https://github.com/zhanxw/rvtests/releases/download/v2.1.0/rvtests_linux64.tar.gz; \ tar zxvf rvtests_linux64.tar.gz; \ ./executable/rvtest --inVcf WES_c${i}_qc_pass.vcf.gz --freqUpper 0.05 \ --pheno m2_pheno_bur_ord.txt --pheno-name copd_only...