Added ~150 segmental duplication regions for GRCh38
Improved gene callers
F8: Improved calling of Intron22 inversion and Exon1-22 deletion
NCF1: Improved assignment of genes to NCF1 vs. pseudogenes
PMS2: Improved assignment of genes to PMS2 vs. pseudogene. Updated the coordinates of the region to phase
IKBKG: Improved assignment of genes to IKBKG vs. pseudogene. Updated the coordinates of the region to phase
RCCX: Better calling of a multi-allelic site IVS2-13A/C>G
CFC1: Updated the coordinates of the region to phase
For SMN1/STRC/PMS2/IKBKG/NCF1, variants are now called against the gene for gene haplotypes and against the paralog/pseudogene for paralog/pseudogene haplotypes
Report F8 Intron 22 inversion and Exon1-22 deletion, and IKBKG 11.7kb deletion in VCFs
Improved homopolymer/simple repeat masking before phasing
Included filtered calls in VCFs
Added GRCh37/hg19 support for 11 medically relevant gene families
This is Version 3.0.0 Summary of changes: