1be8a88909
1) GATKArgumentCollection has a command to turn off randomization if setting the seed isn't enough. Right now it's only hooked into RankSumTest. 2) RankSumTest now can be passed a boolean telling it whether to use a dithering or non-randomizing comparator. Unit tested. 3) VariantsToBinaryPed can now output in both individual-major and SNP-major mode. Integration test. 4) Updates to PlinkBed-handling python scripts and utilities. 5) Tool for calculating (LD-corrected) GRMs put under version control. This is analysis for T2D, but I don't want to lose it should something happen to my computer. |
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