rvtests
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zhanxw
Rare variant test software for next generation sequencing data
Dear developers, we are running a big meta-analysis in which most studies are population-based, but also some family-based studies are included. As more than 30 studies including biobanks are part...
Hi, thank your for writing rvtests. A quick question: if the `setFile` format - half-closed 0-based like bed ? - or open 1-based like gtf/gff ? And in the refFlat...
Hi, There seem to be a problem with running the following script below when I apply a --freqUpper filter of 0.01 or 0.05. The script would run without a problem...
Hi, I am getting the full range of covariate results in the output from the SKAT and Burden test. Is there any option to hide the covariate effect from the...
The produced executable is actually `executable/rvtest`
I was checking the log files after creation of the kinship matrices I noticed a warning NOTE: In hemizygous region, males have [ 4870 ] missing genotypes and [ 4870...
Hi there, After running SKAT-O, the output has some columns that I would like to understand better: NumVar: number of variants in the gene (or site) NumPolyVar: number of Polymorphic...
Most of gene-level outputs are reasonable, but there are a few lines show "-nan" in Pvalue. ### Gene RANGE N_IN--geneFile ${geneF} --kernel skato FORMATIVE NumVar NumPolyVar Q rho Pvalue ILF2...
Hi, I am trying to run an analysis for ~5k samples and I've got the time limit of 48 hours, what's your advice? Tried --Numthreads 48 , but this didn't...
I'm in university central IT and we've been asked to install this software for use in teaching. This repo doesn't have a license specified so we can't currently do this....
