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KATK: Fast genotyping of rare variants directly from unmapped sequencing reads
Author(s) -
Kaplinski Lauris,
Möls Märt,
Puurand Tarmo,
Pajuste FannyDhelia,
Remm Maido
Publication year - 2021
Publication title -
human mutation
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.981
H-Index - 162
eISSN - 1098-1004
pISSN - 1059-7794
DOI - 10.1002/humu.24197
Subject(s) - biology , genotyping , false discovery rate , computational biology , genetics , dna sequencing , genotype , gene
KATK is a fast and accurate software tool for calling variants directly from raw next‐generation sequencing 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 the 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. 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.