<i>bamSliceR</i>: a Bioconductor package for rapid, cross-cohort variant and allelic bias analysis.

ABSTRACT: The NCI Genomic Data Commons (GDC) provides controlled access to sequencing data from thousands of subjects, enabling large-scale study of impactful genetic alterations such as simple and complex germline and structural variants. However, efficient analysis requires significant computational resources and expertise, especially when recalling variants from raw sequence reads. We thus developed bamSliceR , an R/Bioconductor package that builds upon the GenomicDataCommons package to extract aligned sequence reads from cross-GDC meta-cohorts, followed by targeted analysis of variants and effects (including transcript-aware variant annotation from transcriptome-aligned GDC RNA data). Here we demonstrate population-scale genomic & transcriptomic analyses with minimal

SUBMITTER: Huang YP 

PROVIDER: S-EPMC10516001 | biostudies-literature | 2024 Nov

REPOSITORIES: biostudies-literature