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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 16 of 305 min read

14. The Germline Pipeline: HaplotypeCaller & Joint Calling

14.1 Single Sample Calling with HaplotypeCaller The flag is critical and deserves dedicated explanation: rather than producing a final, filtered VCF directly, this mode produces a GVCF (Genomic VCF) — a per sample…

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