PT  - JOURNAL ARTICLE
AU  - Fanny-Dhelia Pajuste
AU  - Lauris Kaplinski
AU  - Märt Möls
AU  - Tarmo Puurand
AU  - Maarja Lepamets
AU  - Maido Remm
TI  - FastGT: from raw sequence reads to 30 million genotypes in less than an hour
AID  - 10.1101/060822
DP  - 2016 Jan 01
TA  - bioRxiv
PG  - 060822
4099  - http://biorxiv.org/content/early/2016/06/27/060822.short
4100  - http://biorxiv.org/content/early/2016/06/27/060822.full
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.