This repository contains the files and scripts used for the WES analysis presented in:
Lettera et al., 2025
Molecular and phenotypic blueprint of the hematopoietic compartment reveals proliferation stress as a driver of age-associated human stem cell dysfunctions
#Study Context
## Study Context
Whole-exome sequencing (WES) was performed to evaluate potential genomic alterations in human hematopoietic stem cells during aging. The analysis focused on variant detection and functional annotation.
#Repository Description
## Repository Description
OncoPrint.R: contains the code to process, filter, and create an oncoprint plot from VCF files.
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@@ -21,11 +21,11 @@ Mutect2_variants.txt: contains the already computed and filtered matrix of varia
VarDict_variants.txt: contains the already computed and filtered matrix of variants called using the VarDict pipeline.
#Data Availability
## Data Availability
Raw FASTQ files are available in the European Nucleotide Archive (ENA), accession code: PRJEB93902.
#Tools and Notes
## Tools and Notes
Variants are called using both Mutect2 and VarDict to select a set of high-confidence variants.
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@@ -33,7 +33,7 @@ Variants were then filtered for quality, coverage, presence in a panel of genes
The oncoprint was generated using the ComplexHeatmap R package to explore variant distributions across genes and samples.
