rvtests
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zhanxw
Rare variant test software for next generation sequencing data
Hi, I've encountered a warning and error in rvtests log when I try to conduct a GWAS. My code looks like this: ``` ./software/rvtests/v2.1.0/executable/rvtest \ --inVcf ./derived_data/genetic_data/30_chr12.imputed.poly.vcf.gz \ --dosage DS...
Hi, I have this error fatal: Not a git repository (or any of the parent directories): .git make -C /opt/install-bin/rvtests-master/src release fatal: Not a git repository (or any of the...
- Update eigen download URL to gitlab - update paths because tarball structure has changed - remove reference to file that doesn't exist in vcftools createBCF2Index I saw that a...
Dear @zhanxw, I have been working with rvtests for the past few months and it works well on my large scale WES. I have a question regarding permutations on SKAT-O....
Hi Xiaowei, vcf2kinship support bgen format as input or not? ``` The following parameters are available. Ones with "[]" are in effect: Available Options Input/Output: --inVcf [], --out [] Chromsome...
Hello, I have a dataset with both common and rare variants. Is there a way to simultaneously test them both? How exactly is the grouping data for rare variants formatted?
Hi xiaowei， I am trying to perform gene based association analysis by rvtest ,but i got some error message. My command line is below, as well as error message.And the...
Just to be sure, if I use the same .txt file (tab delimited, with correct column headers etc.) as the phenotype file and covariate file, do I use --sex (which...
Dear Xiaowei, I ran an analysis with score method, loading a kinship matrix and with a binary outcome (sorry I always work with continuous variables so I did not know...
Dear professor, Thank you for your powerful tool. Is it possible to perform rare germline copy number variation analysis with your rvtests. Or would you please provide some suggestion for...
