Uploaded August 2025 | Updated September 2026, 11 hours ago
Get comprehensive HiFi variant discovery—SNVs, indels, SVs, CNVs, tandem repeats, paralog genotypes, *plus 5mCpG methylation—without wiring together a dozen tools yourself.* This WDL pipeline unifies *pbmm2, DeepVariant, GLnexus, Sawfish, TRGT, Paraphase, HiPhase, StarPhase/PharmCAT, and pb-CpG-tools* to deliver analysis-ready outputs on-prem or in the cloud; typical runs finish in *under 12 hours* (resource-dependent).
*Why it matters*
* Reveals variants in more than 400 medically relevant genes in dark regions that short reads often miss.
* Includes methylation every run, so you see variation and regulation together.
* Produces phased VCFs and haplotagged alignments that aid interpretation and IGV review.
*What you’ll learn*
* How the single-input workflow stitches the full toolchain and applies best practices.
* Exactly what you get back: phased alignments with methylation probabilities, small variants, SVs/CNVs, TRGT repeats, PGx diplotypes, summaries.
* Flexible deployment: Cromwell/miniwdl + Docker/Singularity, or managed/cloud (AWS, Azure, GCP, partners).
*Chapters*
00:00 Intro: HiFi WGS variant pipeline overview
00:18 PacBio HiFi sequencing platforms (Vega & Revio systems)
00:45 Why HiFi — a more complete genome view
01:57 Solving the analysis integration challenge
02:41 Pipeline workflow and outputs
03:17 Key tools (DeepVariant, Sawfish, TRGT, etc.)
05:58 Flexible deployment (on-prem & cloud)
06:29 Research impact: rare disease & pedigrees
*Resources*
Human WGS Variant Pipeline code: github.com/PacificBiosciences/HiFi-human-WGS-WDL
PacBio tools: github.com/PacificBiosciences
Learn more about PacBio: pacb.com
Legal & trademarks: pacb.com/legal-and-trademarks
*Subscribe for more PacBio genomics content:*
youtube.com/@PacificBiosciences?sub_confirmation=1
Got questions or a tool you want supported next? *Comment below* and we’ll tackle it in a future video.
#PacBio #HiFiSequencing #VariantCalling
Get comprehensive HiFi variant discovery—SNVs, indels, SVs, CNVs, tandem repeats, paralog genotypes, *plus 5mCpG methylation—without wiring together a dozen tools yourself.* This WDL pipeline unifies *pbmm2, DeepVariant, GLnexus, Sawfish, TRGT, Paraphase, HiPhase, StarPhase/PharmCAT, and pb-CpG-tools* to deliver analysis-ready outputs on-prem or in the cloud; typical runs finish in *under 12 hours* (resource-dependent).
*Why it matters*
* Reveals variants in more than 400 medically relevant genes in dark regions that short reads often miss.
* Includes methylation every run, so you see variation and regulation together.
* Produces phased VCFs and haplotagged alignments that aid interpretation and IGV review.
*What you’ll learn*
* How the single-input workflow stitches the full toolchain and applies best practices.
* Exactly what you get back: phased alignments with methylation probabilities, small variants, SVs/CNVs, TRGT repeats, PGx diplotypes, summaries.
* Flexible deployment: Cromwell/miniwdl + Docker/Singularity, or managed/cloud (AWS, Azure, GCP, partners).
*Chapters*
00:00 Intro: HiFi WGS variant pipeline overview
00:18 PacBio HiFi sequencing platforms (Vega & Revio systems)
00:45 Why HiFi — a more complete genome view
01:57 Solving the analysis integration challenge
02:41 Pipeline workflow and outputs
03:17 Key tools (DeepVariant, Sawfish, TRGT, etc.)
05:58 Flexible deployment (on-prem & cloud)
06:29 Research impact: rare disease & pedigrees
*Resources*
Human WGS Variant Pipeline code: github.com/PacificBiosciences/HiFi-human-WGS-WDL
PacBio tools: github.com/PacificBiosciences
Learn more about PacBio: pacb.com
Legal & trademarks: pacb.com/legal-and-trademarks
*Subscribe for more PacBio genomics content:*
youtube.com/@PacificBiosciences?sub_confirmation=1
Got questions or a tool you want supported next? *Comment below* and we’ll tackle it in a future video.
#PacBio #HiFiSequencing #VariantCalling
