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NGS Analysis30 chapters

11. Where Part 2 Picks Up
12. Variant Calling Fundamentals
13. Core Variant Callers: GATK, DeepVariant, Sentieon, FreeBayes, Strelka
14. The Germline Pipeline: HaplotypeCaller & Joint Calling
15. The Somatic Pipeline: Mutect2, VarScan2, Strelka2, LoFreq
16. Structural Variant Calling: Manta, Delly, Lumpy
17. CNV Calling: CNVkit, Control-FREEC, ExomeDepth, XHMM
18. Gene Fusion Detection: STAR-Fusion, FusionCatcher, Arriba
19. End of Part 2 — Where We've Arrived
Coming in Part 3

/NGS Analysis/Part 2 — Variant Calling: SNVs, Indels, CNVs, Fusions & Structural Variants

Chapter 17 of 305 min read

15. The Somatic Pipeline: Mutect2, VarScan2, Strelka2, LoFreq

15.1 What Makes Somatic Calling Different (Restated With Practical Weight) Somatic calling must reliably distinguish three categories at every candidate site: (1) true somatic variants (present only in tumor/diseased…

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