Tag: annotation

How to take a raw whole-genome VCF, normalize it correctly, annotate it with VEP plus population and clinical databases, and flatten it into a table you can query in seconds.

A practical workflow for going from an rsID to a genotype you can trust: resolving coordinates, querying your VCF, falling back to the reads when the VCF is silent, and annotating the result correctly.

A step-by-step pipeline for taking a 4-5 million variant single-sample VCF and reducing it to a few dozen candidates, with the actual bcftools, ANNOVAR, and slivar commands, plus where the filters lie to you.

A working guide to turning RNA-seq quantifications into an annotated, versioned gene table: choosing an annotation, building tx2gene, attaching biotypes and symbols, functional mapping, and cell-type annotation for single-cell data.

What is in a VCF, how to filter it down to variants worth reading, how to read a single variant end to end, and what a negative result does not rule out.

A genome report is a filtered summary built on top of your variant calls. Here is what goes into one, which files matter more than the PDF, and what sequencing costs in 2026.

A working setup for looking up any SNP in your own sequencing data: normalize and index the VCF, annotate with rsIDs and consequences, verify the genotype in the raw reads, and query millions of variants in under a second.

A working stack for analyzing your own whole-genome sequencing data: alignment with BWA-MEM2 or Dragen, variant calling with DeepVariant, annotation with VEP, and interpretation limits you should respect.

A practical guide to resolving rsIDs against your own genotypes: normalizing a VCF, querying dbSNP and Ensembl, annotating with consequence, frequency, and ClinVar, and reading the result without over-interpreting it.

A working guide to variant interpretation software: what each layer of the stack does, which tools we would use for a personal whole genome, and where the interpretation breaks.

A working guide to calling, normalizing, annotating, and querying SNPs from your own sequencing or array data, with the specific tools, flags, and failure modes that matter.

A working pipeline for annotating a personal whole-genome VCF: normalize with bcftools, annotate with Ensembl VEP offline, join custom datasets with vcfanno or slivar, then filter down to something you can read.

A working guide to reading, normalizing, filtering, annotating, and querying a Variant Call Format file from whole-genome sequencing, including how to get a slice of it into a spreadsheet without breaking it.

A working guide to the free DNA upload sites worth using, what each one does with your file, and how to run the same annotation, polygenic scoring, and relative-matching analyses yourself on your own machine.

A working guide to interpreting raw genotype files from 23andMe or Ancestry, converting them to VCF, annotating variants, and knowing where array data stops being useful.

A working guide to taking a 23andMe/Ancestry export or a whole-genome FASTQ, converting it to an annotated VCF, filtering it sensibly, and knowing which results are real.