bgen utilities in executable binary files

[ppjeep]

1. Could you please add bgen2vcf, bgenFileInfo utitlies into pre-built executable binary package (for Linux 64bit)?

2. In the example folder of rvtest package, you did not specify --freqUpper 0.05 in cmd.sh. Here is the example code. If I use --freqUpper 0.05 in the same command, the gene based results will be different. Is it OK if I run gene based analysis without using --freqUpper 0.05?
   ../executable/rvtest --pheno pheno --inVcf example.vcf.gz --setFile setFile --burden cmc,cmcWald,zeggini,zegginiWald --out out9

3. Summary statistics and covariance matrices of score statistics generated by rvtests meta-analysis models do NOT work with raremetal (v.4.14.1; https://github.com/traxexx/Raremetal). By the way, here I am talking about command line version of raremetal (i.e, it is NOT R package of meta-analysis program). For example, the following example dataset is generated by rvtests, but it cannot be used in raremetal (v.4.14.1; https://github.com/traxexx/Raremetal)

Here is a list of commands for the third question.

example dataset

http://genome.sph.umich.edu/wiki/RareMETALS2

$ more example.summary.files

example1.MetaScore.assoc.gz

example2.MetaScore.assoc.gz

[zhangh13@headnode try_meta]$ more example.cov.files
###example1.MetaCov.assoc.gz

example2.MetaCov.assoc.gz

#!/bin/bash
raremetal --summaryFiles example.summary.files --covFiles example.cov.files --prefix out_example
raremetal --summaryFiles example.summary.files --covFiles example.cov.files --writeVcf --prefix example_pool
bgzip example_pool.pooled.variants.vcf
tabix -pvcf -f example_pool.pooled.variants.vcf.gz
epacts anno --in example_pool.pooled.variants.vcf.gz --out example_pool.pooled.variants_epacts_anno.vcf.gz
gunzip example_pool.pooled.variants_epacts_anno.vcf.gz
raremetal --summaryFiles example.summary.files --covFiles example.cov.files --annotatedVcf example_pool.pooled.variants_epacts_anno.vcf --burden --MB --SKAT --VT --prefix out_example_epacts_anno