iCopyDAV: Integrated platform for copy number variations-Detection, annotation and visualization.
Prashanthi DharanipragadaSriharsha VogetiNita ParekhPublished in: PloS one (2018)
Discovery of copy number variations (CNVs), a major category of structural variations, have dramatically changed our understanding of differences between individuals and provide an alternate paradigm for the genetic basis of human diseases. CNVs include both copy gain and copy loss events and their detection genome-wide is now possible using high-throughput, low-cost next generation sequencing (NGS) methods. However, accurate detection of CNVs from NGS data is not straightforward due to non-uniform coverage of reads resulting from various systemic biases. We have developed an integrated platform, iCopyDAV, to handle some of these issues in CNV detection in whole genome NGS data. It has a modular framework comprising five major modules: data pre-treatment, segmentation, variant calling, annotation and visualization. An important feature of iCopyDAV is the functional annotation module that enables the user to identify and prioritize CNVs encompassing various functional elements, genomic features and disease-associations. Parallelization of the segmentation algorithms makes the iCopyDAV platform even accessible on a desktop. Here we show the effect of sequencing coverage, read length, bin size, data pre-treatment and segmentation approaches on accurate detection of the complete spectrum of CNVs. Performance of iCopyDAV is evaluated on both simulated data and real data for different sequencing depths. It is an open-source integrated pipeline available at https://github.com/vogetihrsh/icopydav and as Docker's image at http://bioinf.iiit.ac.in/icopydav/.
Keyphrases
- copy number
- genome wide
- high throughput
- mitochondrial dna
- deep learning
- electronic health record
- big data
- loop mediated isothermal amplification
- label free
- real time pcr
- machine learning
- dna methylation
- low cost
- convolutional neural network
- gene expression
- high resolution
- endothelial cells
- combination therapy
- rna seq
- replacement therapy
- sensitive detection
- single molecule
- smoking cessation
- quantum dots