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eXome Hidden Markov model (XHMM) - Copy Number Variants (CNVs) from Whole Exome Sequencing Data Topics

What does a "typical" XHMM workflow look like? the "best practice" bwa + Picard + GATK pipeline, though variations on this pipeline, successfully employed by various users. For …

XHMM uses principal component analysis (PCA) normalization and a hidden Markov model (HMM) to detect and genotype copy number variation (CNV) from normalized read-depth data …

2021年10月10日 · XHMM 是一个用PCA降噪+HMM方法来检测全外显子CNV的软件。 软件 文档 可在这里查看。 XHMM安装依赖GCC 4.4以上，以及 pthread 和 lapack。 安装比较麻烦，可 …

A Hidden Markov Model (HMM) can be used to explore this scenario. We don't get to observe the actual sequence of states (the weather on each day). Rather, we can only observe some …

Change to the xhmm directory: . Run make to install the software (which starts by automatically compiling the included hmm++ library): . The XHMM R code is now available as an R library. …

2021年1月19日 · xhmm是用于wes数据的cnv分析工具，通过pca归一化测序深度，结合隐马可夫模型进行cnv预测。流程包括比对参考基因组、归一化、构建hmm模型及cnv调用。pca有助于减 …

Discovery of copy number variations (CNVs) from exome read depth using XHMM (eXome-Hidden Markov Model)

XHMM uses principal component analysis (PCA) normalization and a hidden Markov model (HMM) to detect and genotype copy number variation (CNV) from normalized read-depth data …