AMAP: A pipeline for whole-genome mutation detection in Arabidopsis thaliana
AMAP: A pipeline for whole-genome mutation detection in Arabidopsis thaliana
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DOI：
10.1266/ggs.15-00078
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发表时间：
2016-08-01
影响因子：
1.1
通讯作者：
Abe, Tomoko
中科院分区：
文献类型：
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作者：
Ishii, Kotaro;Kazama, Yusuke;Abe, Tomoko
通过使用高通量测序，现在可以在全基因组水平上检测突变。然而，由于突变检测程序提供的假阳性数量，确定突变是一个耗时的过程。AMAP（自动突变分析管道）的开发就是为了解决这个问题。AMAP集成了一套经过充分验证的程序，用于映射（BWA）、去除潜在的PCR重复（Picard）、重新比对（GATK）和突变检测（SAMtools、GATK、Pindel、BreakDancer和CNVnator）。因此，所有类型的突变，如碱基取代，缺失，插入，易位和染色体重排可以通过AMAP检测。此外，AMAP通过比较测序突变体中的候选突变列表来自动区分假阳性。我们通过输入已经分析的来自三个单独的拟南芥突变体的读段数据来测试AMAP，并确认所有真实突变都包括在候选突变的列表中。结果表明，假阳性的数量减少到12%，在以前的分析，缺乏减少假阳性的过程中获得的。因此，AMAP不仅将加速单个诱变剂的突变诱导分析，而且还将加速正向遗传学的过程。
Detection of mutations at the whole-genome level is now possible by the use of high-throughput sequencing. However, determining mutations is a time-consuming 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.