Tag: germline analysis
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How To Analyze Whole Genome Sequencing Data For Absolute Beginners Part 6: Identifying Germline Copy Number Variants
Introduction: Understanding Copy Number Variants While single nucleotide variants (SNVs) and small insertions/deletions (indels) capture much of the attention in genomic analysis, they represent only part of the story of human genetic variation. Copy Number Variants (CNVs) – duplications and deletions of large segments of DNA – play an equally important role in human genetics,
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Alternative Splicing Analysis ATAC-seq BAM cancer genomics 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 somatic mutations Transcript VCF whole genome sequencing