MADSEQ-package: Mosaic Aneuploidy Detection using Massive Parallel Sequencing...

In MADSEQ: Mosaic Aneuploidy Detection and Quantification using Massive Parallel Sequencing Data

Description

The MADSEQ package provides a group of hierarchical Bayesian models for the detection and quantification of mosaic aneuploidy using massive parallele sequencing data.

Details

MADSEQ is a group of hierarchical Bayesian models used for the detection and quantification of mosaic aneuploidy. The package takes bam file and vcf file as input. There are functions for the calculation of the coverage for the sequencing data; the normalization of the coverage to correct GC bias; the detection and quantification of mosaic aneuploidy and the inference of the type of aneuploidy (monosomy, mitotic trisomy, meiotic trisomy, loss of heterozygosity). The package also includes function to visualize the estimated distribution for detected mosaic aneuploidy. To fully understand how to use the MADSEQ package, please check the documentation. The manual explains what data do you need, and how to process the data to be ready for the model, what steps to follow and how to interpret the output from our model.

Author(s)

Yu Kong

References

Martyn Plummer (2016). rjags: Bayesian Graphical Models using MCMC. R package version 4-6. http://CRAN.R-project.org/package=rjags
C. Alkan, J. Kidd, T. Marques-Bonet et al (2009). Personalized copy number and segmental duplication maps using next-generation sequencing. Nature Genetics, 41(10):1061-7.

MADSEQ documentation built on Nov. 8, 2020, 6:51 p.m.