Tag: contamination assessment
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How To Analyze Whole Genome Sequencing Data For Absolute Beginners Part 2A: Matched Tumor-Normal Mutation Calling With Mutect2
Introduction to Matched Tumor-Normal Analysis Welcome back to our whole genome sequencing analysis journey! In Part 1, we learned how to process raw sequencing data and identify germline variants using GATK’s best practices. Now we’re ready to tackle the gold standard approach for detecting somatic mutations: matched tumor-normal analysis. What Are Somatic Mutations? Somatic mutations
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Alternative Splicing Analysis ATAC-seq BAM ChIP-seq chromatin accessibility CNV DESeq2 Differential Expression edgeR FASTQ GATK Mutect2 gene expression heatmap HOMER HPC Isoform limma MACS2 MAF miRNA miRNA-seq MSigDB Normalization peak calling RNA-seq SLURM somatic mutations Transcript VCF whole genome sequencing