PT  - JOURNAL ARTICLE
AU  - Lauris Kaplinski
AU  - Märt Möls
AU  - Tarmo Puurand
AU  - Fanny-Dhelia Pajuste
AU  - Maido Remm
TI  - KATK: fast genotyping of rare variants directly from unmapped sequencing reads
AID  - 10.1101/2020.12.23.424124
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.12.23.424124
4099  - http://biorxiv.org/content/early/2020/12/23/2020.12.23.424124.short
4100  - http://biorxiv.org/content/early/2020/12/23/2020.12.23.424124.full
AB  - Motivation KATK is a fast and accurate software tool for calling variants directly from raw NGS reads. It uses predefined k-mers to retrieve only the reads of interest from the FASTQ file and calls genotypes by aligning retrieved reads locally. KATK does not use data about known polymorphisms and has NC (No Call) as default genotype. The reference or variant allele is called only if there is sufficient evidence for their presence in data. Thus it is not biased against rare variants or de novo mutations.Results With simulated datasets, we achieved a false negative rate of 0.23% (sensitivity 99.77%) and a false discovery rate of 0.19%. Calling all human exonic regions with KATK requires 1-2 h, depending on sequencing coverage.Availability KATK is distributed under the terms of GNU GPL v3. The k-mer databases are distributed under the Creative Commons CC BY-NC-SA license. The source code is available at GitHub as part of Genometester4 package (https://github.com/bioinfo-ut/GenomeTester4/). The binaries of KATK package and k-mer databases described in the current paper are available on http://bioinfo.ut.ee/KATK/.Competing Interest StatementThe authors have declared no competing interest.