RT Journal Article SR Electronic T1 FastGT: from raw sequence reads to 30 million genotypes in less than an hour JF bioRxiv FD Cold Spring Harbor Laboratory SP 060822 DO 10.1101/060822 A1 Fanny-Dhelia Pajuste A1 Lauris Kaplinski A1 Märt Möls A1 Tarmo Puurand A1 Maarja Lepamets A1 Maido Remm YR 2016 UL http://biorxiv.org/content/early/2016/06/27/060822.abstract AB 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.