I have my WGS - what next?

#1

My whole genome is sequenced and the files are ready to download.

I am reasonably proficient with R/RStudio. With some review, I could probably resurrect some python skills. I use Claude but only $20 / month version.

The reports that came with the sequencing are useless. What projects should I start with to analyze my data?

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#2
  • Alignment to T2T-CHM13 (via minimap2 or pbmm2, skipping BQSR).
  • Deep-Learning SNV/Indel Calling (via DeepVariant or Clair3).
  • Haplotype Phasing (via WhatsHap for cis/trans structural context).
  • Complex SV & STR Profiling (via Sniffles2 for structural variants + TRGT for tandem repeats).
  • Full-Spectrum Annotation (gnomAD v4, ClinVar, AlphaMissense, plus AnnotSV for long-read structures).
  • Custom Phenotype Filtering (via Slivar with specific biohacker logic/JavaScript).
  • Manual IGV Verification (Focusing on long-read soft-clipping at critical loci).
  • RAG-LLM Literature Association (Feeding phased VCF data to generate optimized, weighted lifestyle reports).

This is the overall rough workflow.

#3

Here is what @cl-user is doing… I recommend you review all his posts on the topic:

#4

@Cole many thanks for the reply. Let me a take some time to digest so I can respond intelligently.

#5

@RapAdmin thank you for your reply. I am very impressed with cl-users work. I think I have a some ways to go in understanding the science of genetic pathways. Little by little I hope to get there.

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