v2.0.0

• 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_by parameter 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 freq parameter: instead than a vcf file now it takes in input a precomputed plink2 freq file
• Default number of permutations changed from 10 to 100

Full Changelog: 1.0.7...2.0.0

v1.0.7

Corrects a bug in the testing profile that was causing the minP process to fail with --profile test

v1.0.6

output original matrices

v1.0.5

Added use_dosage parameter to select weather hard-calls or dosages should be used. This tweaks how the vcf is converted to pgen in VCF_TO_PGEN and how the calls are read in FIT_MODEL.

v1.0.4

Added possibility to exclude variants with MAF under a user-specified threshold (--maf_min parameter).

v1.0.3

Minor fixes and enhancements

• Resolved bug in relatedness matrix plotting color range
• Changed the formatting and filename of the GWAS tabular output so that it can be directly loaded in IGV
• Added name at the top of the relatedness matrix and QQ plots
• Made process tags more informative

v1.0.2

Bug fix. NAs in covar or qcovar were causing a failure in the GET_DESIGN_MATRIX process.

v1.0.1

Removed a typo in the path for the output folder where the relatedness matrix heatmaps are published

v1.0.0

First working version of the pipeline