rvtests

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Running rvtests with 1000 Genomes Project Phase 3 dataset

1

Hello, I am using 1000 Genomes files downloaded from [here](ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/) to perform single variant tests. Using the chr20 VCF.GZ file and appropriate PED file the rvtests exits with the following...

NemanjaV

Specify specific variants in group file

2

Hi @zhanxw, Is it possible to specify specific variants in each group (for example epacts format like), other than just specify by range? It's better to have chr:pos:ref:alt like format...

wavefancy

Specify snp weight in grouping test

1

Hi Developers, Is it possible to specify the snp weight for each snp in the grouping rare test. Can we ask for the new feature if there's no. Thanks much...

wavefancy

segmentation fault using SKAT with large data set

1

I'm attaching a backtrace from gdb: (gdb) where #0 0x00002aaaab9e91f7 in raise () from /lib64/libc.so.6 #1 0x00002aaaab9ea8e8 in abort () from /lib64/libc.so.6 #2 0x00002aaaaaf7c1d5 in __gnu_cxx::__verbose_terminate_handler () at ../../../../libstdc++-v3/libsupc++/vterminate.cc:95 #3...

rjbohlender

[ERROR] Cannot specify both gene file and set file

1

Hi, everyone. I have an error "[ERROR] Cannot specify both gene file and set file" when doing setbased analysis. my set file is : ` phosphatases chr3:190282078-190347307` my geneFile is...

weizhousjtu

[ERROR] Error loading gene file or gene list is empty!

1

Hi! I usually run rvtests for rare variant testing with no problems at all. However, only for some genes, I've been getting the following error message: ``` [INFO] Analysis begins...

MDiezFairen

Compilation issues and segmentation faults

2

We're unable to compile rvtests on our Linux cluster. We've tried compiling under three different compiler combinations on our system and each time we get a series of compile errors...

kassaq

Segmentation fault when using --vt price

1

Hello, I usually run rvtest on a linux cluster, but want to add mac compatibility to my workflow. I downloaded the latest release of RVtests and am trying to run...

Thatguy027

Change in versioning scheme intentional?

1

Hello, The most recent version of rvtests switches from a classic dot-style versioning scheme (2.0.7) to a date-style versioning scheme (20181226). Is that intentional, or did it happen in error?...

epruesse

Segmentation fault for score test (v20181226)

1

Hi ! when running the new version (20181226) with the --single score, it is always giving ma a segmentation fault. Could you please try and see whether there is an...

winkusch