Tag: vcf

A gene panel is a subset of an exome, and an exome is about 1.5% of a genome. Here's how the three differ in coverage, cost, file sizes, and what you can re-analyze later.

A genome explorer is a coordinate browser plus a query layer over your own alignments and variant calls. Here is the stack we would use on a personal 30x whole genome, with the commands, file formats, and failure modes.

"Genome manager" usually means a vendor's web portal for your sequencing results. Here is what that portal does, what it hides, and how to run your own catalog of VCFs, BAMs, expression matrices, and lab panels with tools you already know.

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.

How to download the raw genotype file, convert it to VCF against a reference, lift it to GRCh38, impute, score, and know which conclusions the array can and cannot support.

Most consumer wellness DNA tests report array genotypes and low-evidence trait associations. Here is what a genome can and cannot tell a healthy person, which file formats and tools matter, and where the real signal is.

A working guide to lifting positions, VCFs, intervals, and probe manifests between GRCh37, GRCh38, and T2T-CHM13, including which tool to use for each file type and how to tell when the lift silently went wrong.

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.

What whole-genome sequencing results contain, which files matter, how to interpret a variant classification, and where the analysis stops and a clinician starts.

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 step-by-step guide to annotating your personal WGS VCF with Ensembl VEP: cache setup, plugin stack (AlphaMissense, CADD, SpliceAI, LOFTEE, dbNSFP), consequence picking, and turning millions of annotated rows into something you can query.

A practical guide to DNA analysis tools: what works on a 23andMe-style genotype file, what requires FASTQ/BAM/VCF from whole-genome sequencing, and the commands we would run at each step.

A step-by-step guide to exporting raw genotype files from Ancestry, 23andMe, and MyHeritage, converting them to a reference-correct VCF, lifting to GRCh38, imputing, and understanding what an array file can and cannot tell you.

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 pipeline for taking a personal WGS VCF into R: GDS conversion, quality metrics, ancestry PCA against 1000 Genomes, variant annotation, and polygenic score computation, with the failure modes that silently corrupt each step.

A practical walkthrough for taking a whole-genome VCF, keeping only the variants your caller flagged as PASS, normalizing them, and flattening the result into a table you can query. Includes the failure modes that silently drop real variants.

A practical guide to ordering whole-genome sequencing for yourself: what coverage and read length to insist on, which files to demand, how to check quality yourself, and what the data can and cannot tell you.

A plain answer to what a genome is, what whole-genome sequencing produces, and how to work with your own FASTQ, CRAM, and VCF files without fooling yourself.

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.

Why genotyping arrays like 23andMe and AncestryDNA answer a narrow question, what whole-genome sequencing gives you instead, and how to work with the files yourself.

DNA.Land stopped accepting uploads and shut down its reports. This guide shows how to take the same raw genotype file, convert it to VCF, impute it, annotate it, and decide which remaining upload sites are worth your data.

What a WGS service delivers, what the files look like, what coverage and platform choices change, and how to tell a real provider from a reseller.

A worked walkthrough of what real DNA results look like: array text files, VCF lines field by field, coverage and callability checks, annotation with VEP, and what a 'positive' result does and does not mean.

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 practical pipeline for turning a tellmeGen raw data export into a build-verified VCF, running quality control, annotating it, and understanding what a genotyping array can and cannot tell you.

A FoundMyFitness report is a literature annotation layer on top of a consumer genotyping array. Here's how to audit the underlying file, rebuild the analysis yourself, and understand where array data runs out.

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 step-by-step method for pulling rs1801133 and rs1801131 out of a 23andMe, AncestryDNA, or WGS file yourself, getting the strand right, and understanding what the result does and does not tell you.

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.