Jonathon LeFaive
Jonathon LeFaive
The reference panel should be phased and most phasing software will impute missing genotypes while phasing.
Note: Minimac4 expects the reference panel to be sourced from whole genome sequence date.
Run "make CFLAGS=-std=c++11" when compiling with clang.
Can you try using the `--ref` option? See `epacts --help` for more information.
It probably hasn't made it to the master branch yet, but this was fixed with https://github.com/statgen/EPACTS/commit/60fe5db5b1f57bfae3e57330bdb7f6729ac0f1e0. I would recommend using the latest pre-release (https://github.com/statgen/EPACTS/releases).
Which analysis are you trying to run? Can you attach the entire log file?
I see. It's because you have the `--anno` option enabled. We will need to add a parameter in `epacts single` for specifying the gene file. In the meantime, you can...
It doesn't. The `initRef` function is called when an alternative reference is provided, which overrides the initial values. See https://github.com/statgen/EPACTS/blob/develop/scripts/epacts.pm#L576-L648.
You can find a build 38 map file at http://csg.sph.umich.edu/locuszoom/download/recomb-hg38.tar.gz
Chances are you need to run `make clean && make` from the source directory. The executable checked into the bin directory is most likely dynamically linked to system libs.