-
Hello,
My command is as follows:
rvtest --inVcf vcf --pheno pheno --covar covariate --out out --kinship kinship.output.kinship --dosage DS --single FamScore
The AF column is 0 for all variants…
-
In `scan1()` and related functions, detect and drop linearly dependent covariate columns **after** dropping individuals that don't appear in all data objects.
For example, if you have batch 2,3,4 ind…
-
Hello all,
I ran into an odd problem when trying to generate a kinship matrix using Rvtest. The dataset I am working on actually consists of two subcohorts that were genotyped and imputed together,…
-
Hi,
I get this error:
gsl: fsolver.c:126: ERROR: endpoints do not enclose a minimum
when running MEN on chr22 (but chrX works).
My command:
rvtest --inVcf "/mnt/isilon/grant_lab/imputation_B…
chesi updated
7 years ago
-
Any way to get peddy to output its kinship estimates to a file? (e.g. king.kin/kin0 equivalent files) I'm trying to investigate whether peddy replicates some *maybe* 2nd-cousin-level relatedness and i…
-
Hi, Xiaowei:
We have prepared tabixed vcf.gz file and PED file and kinship matrix and prepare to run the rvtest. But when we run the rvtest it response the mistake about Segmentation fault as foll…
-
set covariates to 0 or fail?
-
We need to add a MAF / HWE filter for the SNPs.
We might want to think about using filters in the samples based on the kinship.
-
I would like to propose support for Scala-style extractors. What follows is background on why I believe this support is important, and a sketch of how this support could be accomplished. This proposal…
-
Dear Xiaowei
I am using vcf2kinship command to generate kinship matrix, the command are as below:
vcf2kinship --inVcf chrall_notmonomorph.vcf.gz --ped phenotypes_all.ped --bn --minMAF 0.050000 --…