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CNV region plotter from CRAM/BAM files.
cnv-visualizer's Introduction
Use the vizualizeAlignmentsWorkflow.sh for visualizing read coverage.
- Takes as input a cram or bam file
- Makes intermediate file based off of bed file: ivls_of_interest.bed
- Uses bedtools multicov to count alignments from cram overlapping each
interval as specified in the intermediate file created by the workflow
- plotCNV.R takes care of the plotting using ggplot2
- Bedtools
- R: ggplot2
- R: tidyverse
January 2023 - Brady Neeley
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