HAT: de novo variant calling for highly accurate short-read and long-read sequencing data.
HAT: de novo variant calling for highly accurate short-read and long-read sequencing data.
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HAT：从头变体调用，需要高度准确的短读长和长读长测序数据。
DOI：
10.1101/2023.01.27.525940
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发表时间：
2023
期刊：
影响因子：
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通讯作者：
Turner,TycheleN
中科院分区：
文献类型：
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作者：
Ng,JeffreyK;Turner,TycheleN
新变异体（DNV）是存在于后代中但不存在于其亲本中的变异体。DNV对于检查突变率以及鉴定疾病相关变异都很重要。虽然已经做出努力来调用DNV，但从亲子测序的三重数据调用DNV仍然具有挑战性。我们开发了HareAndTorvent（HAT）作为自动化DNV检测工作流程，用于高度准确的短读段和长读段测序数据。可靠的检测DNVs是重要的人类基因组学和HAT地址这一need.ResultsHAT是一个计算工作流程，开始对齐读数据（即CRAM或BAM）从一个亲子测序的三人组和输出DNVs。HAT检测来自Illumina短读全外显子组测序、Illumina短读全基因组测序和高度准确的PacBio HiFi长读全基因组测序数据的高质量DNV。基于一系列质量指标，这些DNV的质量很高，包括每个个体的DNV数量、CpG位点的DNV百分比以及定相到父源染色体的DNV百分比。可用性和实施https：github.com/TNTurnerLab/HAT
Motivationde novovariants (DNVs) are variants that are present in offspring but not in their parents. DNVs are both important for examining mutation rates as well as in the identification of disease-related variation. While efforts have been made to call DNVs, calling of DNVs is still challenging from parent–child sequenced trio data. We developedHareAndTortoise (HAT) as an automated DNV detection workflow for highly accurate short-read and long-read sequencing data. Reliable detection of DNVs is important for human genomics and HAT addresses this need.ResultsHAT is a computational workflow that begins with aligned read data (i.e. CRAM or BAM) from a parent–child sequenced trio and outputs DNVs. HAT detects high-quality DNVs from Illumina short-read whole-exome sequencing, Illumina short-read whole-genome sequencing, and highly accurate PacBio HiFi long-read whole-genome sequencing data. The quality of these DNVs is high based on a series of quality metrics including number of DNVs per individual, percent of DNVs at CpG sites, and percent of DNVs phased to the paternal chromosome of origin.Availability and implementationhttps://github.com/TNTurnerLab/HAT