TY - JOUR T1 - FastGT: from raw sequence reads to 30 million genotypes in less than an hour JF - bioRxiv DO - 10.1101/060822 SP - 060822 AU - Fanny-Dhelia Pajuste AU - Lauris Kaplinski AU - Märt Möls AU - Tarmo Puurand AU - Maarja Lepamets AU - Maido Remm Y1 - 2016/01/01 UR - http://biorxiv.org/content/early/2016/06/27/060822.abstract N2 - We have developed a computational method that counts the frequencies of unique k-mers in FASTQ-formatted genome data and uses this information to infer the genotypes of known variants. FastGT can detect the variants in a 30x genome in less than 1 hour using ordinary low-cost server hardware. The overall concordance with the genotypes of two Illumina “Platinum” genomes is 99.96%, and the concordance with the genotypes of the Illumina HumanOmniExpress is 99.82%. Our method provides k-mer database that can be used for the simultaneous genotyping of approximately 30 million single nucleotide variants (SNVs), including > 23,000 SNVs from Y chromosome. ER -