SV Calling with SVABA | Structural Variants in Cancer скачать в хорошем качестве

SV Calling with SVABA | Structural Variants in Cancer

In this video, I walk through how to perform tumor-normal structural variant analysis using SvABA, a tool designed for sensitive detection of somatic SVs and indels from short-read sequencing data. We start with aligned .bam files from tumor and matched normal samples, run SvABA to identify somatic SVs, and then visualize the results with a customized Circos plot. This workflow is particularly useful in cancer genomics for interpreting complex rearrangements and structural alterations across the genome. What You'll Learn: -Preparing reference files for structural variant calling -Running SvABA for SV calling -Parsing and formatting SV output -Creating Circos plots to visualize genomic rearrangement Tools Used: -SvABA for SV calling -bioconda for installing packages -samtools for reference file indexing -bwa for reference file indexing -circlize to plot the circos plot Code and data used in this tutorial can be found here: https://github.com/garrettc00per/yout... 0:00:00 Introduction 00:10:30 Installing SvABA 00:24:21 Moving WGS Files from S3 to EC2 Instance 00:29:15 Downloading Reference for SV Calling 00:30:51 Moving Reference onto S3 Bucket 00:32:01 Moving Reference from S3 to EC2 Instaqnce 00:33:54 Reference Indexing 00:40:39 Running SvABA 00:43:02 Moving SvABA Output into Local R Environment 00:46:56 SvABA Output Explained 00:53:34 Visualizing SV Data with Circos Plot