Compression/Decompression Method and Apparatus for Genomic Variant Call Data

A data decompression method for decompressing a compressed representation of at least a portion of an individual's genome, comprising:

• receiving the compressed representation;
• accessing a reference database comprising a plurality of reference lists of genetic variants from other individuals, each reference list comprising a sequence of genetic variants from a single, phased haplotype, each variant being defined relative to a reference genome;
• extracting from the compressed representation two mosaics of segments from the reference lists which match the at least a portion of the individual's genome to within a threshold accuracy, each mosaic representing a single one of the two haplotypes of the individual's genome in the at least a portion of the individual's genome, each of the segments comprising a portion of the sequence of genetic variants from one of the reference lists;
• extracting from the compressed representation deviations from the two mosaics exhibited by the at least a portion of the individual's genome;
• and
• decompressing the compressed representation by generating a sequence of variants defined relative to a reference genome that represents the at least a portion of the individual's genome using the extracted two mosaics and the extracted deviations from the two mosaics.

A data processing apparatus configured to generate a compressed representation of at least a portion of an individual's genome, comprising:

• a data interface configured to receive an input file comprising a representation of the at least a portion of the individual's genome in the form of a sequence of variants defined relative to a reference genome;
• a memory device storing a reference database comprising a plurality of reference lists of genetic variants from other individuals, each reference list comprising a sequence of genetic variants from a single, phased haplotype;
• and
• a processing unit configured to:
• identify two mosaics of segments from the reference lists which match the at least a portion of the individual's genome to within a threshold accuracy, each mosaic representing a single one of the two haplotypes of the individual's genome in the at least a portion of the individual's genome for which the compressed representation is to be generated, each of the segments comprising a portion of the sequence of genetic variants from one of the reference lists;
• and
• generate the compressed representation, the generating comprising encoding the two mosaics and deviations from the two mosaics.

A data processing apparatus configured to decompress a compressed representation of at least a portion of an individual's genome, comprising:

• a data interface configured to receive the compressed representation;
• a memory device storing a reference database comprising a plurality of reference lists of genetic variants from other individuals, each reference list comprising a sequence of genetic variants from a single, phased haplotype, each variant being defined relative to a reference genome;
• and
• a processing unit configured to:
• extract from the compressed representation two mosaics of segments from the reference lists which match the at least a portion of the individual's genome to within a threshold accuracy, each mosaic representing a single one of the two haplotypes of the individual's genome in the at least a portion of the individual's genome, each of the segments comprising a portion of the sequence of genetic variants from one of the reference lists;
• extract from the compressed representation deviations from the two mosaics exhibited by the at least a portion of the individual's genome;
• and
• decompress the compressed representation by generating a sequence of variants defined relative to a reference genome that represents the at least a portion of the individual's genome using the extracted two mosaics and the extracted deviations from the two mosaics.