AMAP: A pipeline for whole-genome mutation detection in Arabidopsis thaliana

Kotaro Ishii, Yusuke Kazama, Tomonari Hirano, Michiaki Hamada, Yukiteru Ono, Mieko Yamada, Tomoko Abe

    Research output: Contribution to journalArticle

    4 Citations (Scopus)

    Abstract

    Detection of mutations at the whole-genome level is now possible by the use of high-throughput sequencing. However, determining mutations is a time-consum-ing process due to the number of false positives provided by mutation-detecting programs. AMAP (automated mutation analysis pipeline) was developed to overcome this issue. AMAP integrates a set of well-validated programs for mapping (BWA), removal of potential PCR duplicates (Picard), realignment (GATK) and detection of mutations (SAMtools, GATK, Pindel, BreakDancer and CNVnator). Thus, all types of mutations such as base substitution, deletion, insertion, translocation and chromosomal rearrangement can be detected by AMAP. In addition, AMAP automatically distinguishes false positives by comparing lists of candidate mutations in sequenced mutants. We tested AMAP by inputting already analyzed read data derived from three individual Arabidopsis thaliana mutants and confirmed that all true mutations were included in the list of candidate mutations. The result showed that the number of false positives was reduced to 12% of that obtained in a previous analysis that lacked a process of reducing false positives. Thus, AMAP will accelerate not only the analysis of mutation induction by individual mutagens but also the process of forward genetics.

    Original languageEnglish
    Pages (from-to)229-233
    Number of pages5
    JournalGenes and Genetic Systems
    Volume91
    Issue number4
    DOIs
    Publication statusPublished - 2016

    Fingerprint

    Arabidopsis
    Genome
    Mutation
    Genetic Phenomena
    Genetic Translocation
    Mutagens

    Keywords

    • Arabidopsis thaliana
    • Heavy-ion beam
    • Mutation detection
    • Pipeline
    • Whole-genome re-sequencing

    ASJC Scopus subject areas

    • Molecular Biology
    • Genetics

    Cite this

    AMAP : A pipeline for whole-genome mutation detection in Arabidopsis thaliana. / Ishii, Kotaro; Kazama, Yusuke; Hirano, Tomonari; Hamada, Michiaki; Ono, Yukiteru; Yamada, Mieko; Abe, Tomoko.

    In: Genes and Genetic Systems, Vol. 91, No. 4, 2016, p. 229-233.

    Research output: Contribution to journalArticle

    Ishii, K, Kazama, Y, Hirano, T, Hamada, M, Ono, Y, Yamada, M & Abe, T 2016, 'AMAP: A pipeline for whole-genome mutation detection in Arabidopsis thaliana', Genes and Genetic Systems, vol. 91, no. 4, pp. 229-233. https://doi.org/10.1266/ggs.15-00078
    Ishii, Kotaro ; Kazama, Yusuke ; Hirano, Tomonari ; Hamada, Michiaki ; Ono, Yukiteru ; Yamada, Mieko ; Abe, Tomoko. / AMAP : A pipeline for whole-genome mutation detection in Arabidopsis thaliana. In: Genes and Genetic Systems. 2016 ; Vol. 91, No. 4. pp. 229-233.
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