rvtests
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zhanxw
Rare variant test software for next generation sequencing data
Dear Xiaowei, I want to use `rvtests` to analyze variants data in a non-human data, whose `CHROM` field in the .vcf file is labeled in a different way. ``` #CHROM...
Dear Zhanxw, I tried a SKAT analysis using rvtests for a VCF file containing multiallelic variants. It seems like it almost works but fails just at the end in one...
Hi! I am using the function "vcf2kinship" in rvtest to calculate a kinship matrix, but I am getting the error "Wrong VCF header", and I don't know why, as the...
Hi, This is concerning the output of linear regression which contains the columns: REF ALT AF U V EFFECT 1. It appear that AF is the allele frequency that corresponds...
Hi Xiaowei, Since I started to use rvtests I focused on the Burden test "exactCMC" and on the related single test "exact". The following two questions for you are related...
To whom may it concern, We are using rvtest for genetic associations and noted a problem when doing logistic regression GWAS. Commands where: rvtest --inVcf /home/chr${chr}.dose.vcf.gz --out trialCov_chr${chr} --covar COV.txt...
Hello, while running the command `rvtest --inVcf input.vcf --pheno phenotype.ped --out output --geneFile refFlat_hg19.txt.gz --burden cmc --vt price --kernel skat,kbac` I ran into a segmentation fault. I tried to debug...
Hello, I was wondering if the annotation can be performed using other software like Annovar and still be used to filter based on annotation type with the --annoType filter. Thank...
I used MinGW to compile the source codes directly downloaded from the main page in my windows 10 system. After I type "make" in my command prompt, I got the...
Hi everyone, I am interested in running dominant and recessive meta-analysis tests for burden units instead of single variant but I get only single variant probability values. Is it possible?...
