Tag: vcf

What home genome kits measure, which file formats to insist on, and which variant classes they miss.

A working guide to going from raw whole-genome reads to a filtered, annotated set of single-nucleotide variants you can query, including the tools, flags, quality checks, and the places this pipeline quietly fails.

A genetic report is a short curated document about a handful of variants. The data underneath it is a CRAM and a VCF with about five million variants. Here is how to read both, and how to check the report yourself.

A clinical whole-genome sequencing report is a short curated document about a handful of variants. The FASTQ, CRAM, and VCF behind it contain roughly four to five million. Here is what each one gives you and how to work with the data yourself.

A working pipeline that turns 30x whole-genome FASTQs into a filtered and benchmarked VCF, plus what changes when the variants are somatic.

A working guide to downloading ClinVar, matching it against your own VCF with bcftools, reading review-status stars correctly, and re-checking your variants as classifications change.

A practical pipeline for taking raw DNA data — array export, VCF, or CRAM — and turning it into something you can query, annotate, and trust, plus what the file cannot tell you.

How to pull rs1801133 out of your own VCF without a strand error, what the C677T variant does to the enzyme, and which blood measurements tell you whether it matters for you.

A working guide to going from raw sequencing reads to an annotated, filtered variant list you can reason about: file formats, strand conventions, QC thresholds, annotation commands, and the failure modes that produce confident nonsense.

A practical setup for loading your own WGS alignments, variant calls, and RNA-seq coverage into IGV and igv.js, with the indexing, reference-build, and chromosome-naming details that usually break first.

A working pipeline that classifies the variants in a personal VCF under ACMG/AMP rules, and why automated calls disagree with expert curation.

A working pipeline for searching the 4 to 5 million variants in your genome: annotate, filter to a few dozen candidates, then check each by hand.

A working pipeline that turns a personal whole-genome VCF into an annotated variant table you can query, using VEP, gnomAD and ClinVar.

A practical guide to comparing whole genomes: your VCF against the reference, two callsets of the same sample, your genome against a relative's, and human against other species. Tools, flags, and the failure modes that produce fake differences.

What the five ACMG tiers mean on a BRCA report, how to pull the same calls from your own VCF, and what short-read sequencing misses.

A technical review of consumer and clinical whole genome sequencing: coverage depth, file formats, variant calling limits, and what the data can and cannot tell you.

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. Covers resolving coordinates, querying your VCF and checking the reads.

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 and how to read a single variant end to end. Covers the limits of a negative result.

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. Covers indexing the VCF, annotating with rsIDs and verifying genotypes in the reads.

A step-by-step guide to annotating a personal WGS VCF with Ensembl VEP. Covers cache setup, the plugin stack and consequence picking.

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.