hg19K: addressing a significant lacuna in hg19‐based variant calling

The hg19 assembly of the human genome is the most heavily annotated and most commonly used reference to make variant calls for individual genomes. Based on the phase 3 report of the 1000 genomes project (1000G), it is now well known that many positions in the hg19 genome represent minor alleles. Since commonly used variant call methods are developed under the assumption that hg19 reference harbors major alleles at all the ~3 billion positions, these methods mask the calls whenever an individual is homozygous to the minor allele at the respective positions. Hence, it is important to address the extent and impact of these minor alleles in hg19 from the point of view of individual genomes.