Jonathon LeFaive
Jonathon LeFaive
I'm guessing that libStatGen is being built with `/usr/local/bin/c++` or `/usr/local/bin/g++` and Minimac4 is being built with `/usr/bin/c++`. You might be able to solve this by reconfiguring Minimac4 from the...
New changes should target the develop branch, which no longer uses autotools. Also, can you explain the purpose of having docker images for two different operating systems? I don't think...
I'll look into it. Thanks for reporting. Is there a corresponding csi or tbi index for your vcf file?
The appropriate fix for this and other naming conflicts is to wrap all of libStatGen in a namespace. This would be a breaking change but could be set up to...
Please try v1.0.15, which was just released.
I just set up a clean Centos 7 VM and built/tested libStatgen without issue. Did you do a git pull to get the latest version or did you download a...
You need to add `--rsid` when running minimac4. The reference panel also needs to have RS IDs in the ID column.
I'm assuming you are referring to the 1000 genomes panel. This panel does not have RS IDs. You should be able to get them from the 1000 genomes VCFs on...
If the RS IDs exist in the VCF but not the M3VCF, then I would suggest using https://github.com/Santy-8128/m3vcftools to compress to M3VCF. This tool will copy over the ID column....
SAV will show the most improvement for datasets with large sample sizes that contain either WGS genotypes (GT-only) or imputed genotypes stored as DS or HDS. Non-sparse data can see...