Rare copy number variant analysis in case-control studies using snp array data: a scalable and automated data analysis pipeline.

ABSTRACT:

Background

Rare copy number variants (CNVs) significantly influence the human genome and may contribute to disease susceptibility. High-throughput SNP genotyping platforms provide data that can be used for CNV detection, but it requires the complex pipelining of bioinformatic tools. Here, we propose a flexible bioinformatic pipeline for rare CNV analysis from human SNP array data.

Results

The pipeline consists of two major sub-pipelines: (1) Calling and quality control (QC) analysis, and (2) Rare CNV analysis. It is implemented in Snakemake following a rule-based structure that enables automation and scalability while maintaining flexibility.

Conclusions

Our pipeline automates the detection and analysis of rare CNVs. It implements a rigorous CNV quality control, asses

SUBMITTER: Artaza H 

PROVIDER: S-EPMC11566566 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature