- Major change and simplification in workflow logic with the aim of facilitating future integration of an eQTL branch.
- Change of the permutation approach to be performed on the residuals instead than on the genotypes.
- Deprecation of the
permute_byparameter as grouped permutation are not possible on the low-dimensional projection of the residuals. - Support for more genotype input file formats:
vcf,bcf,pgen/psam/pvar,bgen,bed/bim/fam,ped/map. - Change in the
freqparameter: instead than a vcf file now it takes in input a precomputed plink2freqfile - Default number of permutations changed from 10 to 100
Full Changelog: 1.0.7...2.0.0