rvtests
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zhanxw
Rare variant test software for next generation sequencing data
Dear RvTests team, We are working with the chromosome X result files that were generated with Rvtests and submitted to the GIANT consortium for meta-analysis. We noticed that many of...
Hello, This could sound silly, but could you please provide a detailed description about each column in the output files?, I have read all the documentation but I couldn't find...
Hi this PR is a possible fix for https://github.com/zhanxw/rvtests/issues/133 . But I'm not sure if it's the correct way to do it. Thanks.
hi I am having difficulties running the tool and get the output. The analysis skips all the variants for a gene and doesn't give out any results. Do you know...
Hi, I am trying to run SKAT and SKATO for 20 genes with 105977 samples using the following syntax: rvtest -inVcf input.vcf.gz --pheno All_pheno.ped --pheno-name A --covar All_pheno.ped --covar-name B,C,D,E...
Hello, I am writing to double check the reference allele used when providing the effect size in rvtest summary statistics. The description in the manual reads: "ALT_EFFSIZE: for continuous outcome,...
Under documentation for utility models, I see: > When specifying this, rvtests can output genotypes, phenotype, covariates (if any) and **collapsed genotype** to tabular files However, when I use this...
Hi, find in attachement where rvtest seems stalled/frozen (skato test ?) while there is a small number of variant. ``` $ unzip -l test.zip Archive: test.zip Length Date Time Name...
I performed a CMC Wald burden test on my phenotype "EP" adjusted on 6 covariates : sex, AGE, PC1, PC2, PC3 and BMI. My output shows for each gene 7...
Dear RVtest team, I was wondering whether there would be a way to implement an input file giving user specified weights per variants (calculated from annotation for instance). Best wishes...
