The PR adds a new option, --max-snps, that can be used to change the maximum number of SNPs tested in gbat tests. The default value is kept at 10,000 and this new option enables analysis for larger regions or very densely genotyped datasets. I was not sure if there is a naming convention for options that affect gene-based tests, but I am happy to change the current name if needed.
This has been tested and works when running mBAT-combo on regions with more than 10,000 SNPs.
I also added a minor change to the gcta_build_steps_linux.sh to make and install the Spectra dependency.
Hi,
The PR adds a new option,
--max-snps, that can be used to change the maximum number of SNPs tested in gbat tests. The default value is kept at 10,000 and this new option enables analysis for larger regions or very densely genotyped datasets. I was not sure if there is a naming convention for options that affect gene-based tests, but I am happy to change the current name if needed.This has been tested and works when running mBAT-combo on regions with more than 10,000 SNPs.
I also added a minor change to the
gcta_build_steps_linux.shto make and install the Spectra dependency.See issue: https://github.com/jianyangqt/gcta/issues/49
Thanks, -Jonathan