Tag: bcftools

A practical guide to QUAL, hard filters, and genotype masking with bcftools filter and bcftools view, including the failure modes that silently drop variants from your own genome.

A working guide to bcftools mpileup and bcftools call on a personal 30x whole-genome BAM, including filtering, normalization, BCF versus VCF, and where this pipeline will mislead you.

A working guide to rsIDs: what they mean, how to annotate your own VCF against dbSNP, and how to handle merges and withdrawn records.

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.

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. 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.

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 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.