- fixed a typo in akt relatives output
- fixed a makefile bug, default was not building with optimisations
- better handling of hemizygous genotypes in the pca routine
- added the pedphase command
- documentation improvements
- changed -n to -@ for multi-threading
- added the
-xflag topedphaseto exclude certain chromosomes from phasing
- removed infrequently used subcommands (admix,cluster,mendel,prune,tag,etc)
- version is now added to the header
- readback phased sites now propagate throughout the pedigree for higher phase yield
- pedphase now handles the PS tag correctly
- better error handling when reading the pedigree
- more informative help for pedphase
- added VCF4.3 pedigree parsing
- added unrelated command
- relatives command no longer prints unrelated (see above)
- added the pedphase command
- added --assume-homref flag to pca
- mendel.R tweak
- stdout tweaks
- better error handling in pedigree (.fam) reader
- removed akt ibd
- kin re-factoring
- added
-M 0/1/2for plink/kin/grm kinship calculations - frequencies now read from
-Fargument and-R/-Tnow behave as bcftools - moved kinship calculations into their own class
- reduced memory footprint (at the cost of non-deterministic output ordering)
- removed pairfile option
- users must provide one of -F/-R/-T or use --force
- kin command defaults to calculating allele frequency from data
- changed allele frequency vcf argument to -F
- added a check for 0 samples in akt pca
- initial public release