Gene based tests ignore genes/regions that have more than 10,000 SNPs. I have run into situations where a particular cohort with very dense genotyping fails for large genes even after MAF filtering.
I have added a new option --max-snps that enables the user to change the maximum number of SNPs that can be tested.
Update to build example
When building GCTA, I also noticed that the example steps in docs/build/gcta_build_steps_linux.sh were missing the make and make install commands for Spectra.
New option for gene based tests
Gene based tests ignore genes/regions that have more than 10,000 SNPs. I have run into situations where a particular cohort with very dense genotyping fails for large genes even after MAF filtering.
I have added a new option
--max-snpsthat enables the user to change the maximum number of SNPs that can be tested.Update to build example
When building GCTA, I also noticed that the example steps in
docs/build/gcta_build_steps_linux.shwere missing themakeandmake installcommands for Spectra.PR
See PR https://github.com/jianyangqt/gcta/pull/48 for proposed changes.