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ATLAS / Common Methods: glf format

The fields of the glf format

For a site:

  • recordType: uint8_t = 1 for a SNP entry
  • offset: uint32_t, basically the position
  • maxLL and depth: as one uint32_t, maxLL is in phred and capped at 255
  • root mean square of mapping qualities: uint8_t at the moment not calculated, set to 0 for all
  • genotypeLL: uint8_t x 10, the 10 normalized phred genotype likelihoods

For a new chromosome:

  • recordType: uint8_t = 0 for a chromosome entry
  • chromosome name: uint8_t if it's empty, else uint32_t