Tag: bcftools

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 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 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 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.