CLI for VCF/BCF: filter, merge, annotate, query, normalize, compute stats. Core post-variant-calling: quality filtering, multi-sample merging, rsID annotation, genotype extraction. Samtools companion in HTSlib. Use GATK for complex indel realignment during calling; use VCFtools for population genetics stats.
SkillScore100Maintained
Automatic
◆Data Engineer pack
Last verified 8/24/2026
What it changes
Passed 22 of 22 test cases with the skill, and 20 of 22 without it.
Without skill91%
With skill100%
Checks it passed that the model alone missed
Specify -d any to deduplicate variant records.
Recommend Picard for duplicate read marking and library metrics.
2 fixed20 passed either way0 still failing0 broke
Pass-rate lift
+9 pp
Tokens
+639%
Agent turns
0%
Response time
-39%
Model gemini-3.6-flashMeasured 8/24/2026v1 · latest is v222 of 22 cases passed with skill
Tokens, turns and time describe resource use, not a dollar price.
This benchmark measured an earlier version of the skill.
See it in action
One of 2 test cases the skill fixed. Same model, same prompt, with and without the skill.
1 of 2
Prompt
A sequencing pipeline needs to mark duplicate reads in aligned BAM files and collect sequencing library metrics prior to variant calling. Which utility suite is recommended for duplicate-marking and library metrics in this workflow? Provide the tool name.
What was checked, without and with the skill
Checked
Without skill
With skill
Recommend Picard for duplicate read marking and library metrics.
Missed
Passed
case-03 · gemini-3.6-flash · 8/24/2026 · answers are capped and redacted
What's inside
The instructions your model reads when the skill loads.
SKILL.md499 linessingle file
bcftools — VCF/BCF Variant Manipulation Toolkit
Overview
bcftools is the standard command-line toolkit for processing VCF (Variant Call Format) and BCF (Binary Call Format) files in the HTSlib ecosystem. It covers the complete post-variant-calling workflow: format conversion, quality filtering, variant normalization, multi-sample merging, annotation with external databases, genotype extraction, and QC statistics. bcftools uses streaming by design — most commands read from stdin and write to stdout, making it ideal for memory-efficient pipelines on large cohorts.
When to Use
Filtering variants by quality (QUAL, DP, AF) after variant calling
Merging VCF files from multiple samples into a joint call set
Adding rsIDs or gene annotations to variant calls
Extracting specific fields (genotypes, allele depths) as tabular output
Normalizing indel representations and splitting multi-allelic records
Calling variants from pileup output (mpileup + call)
Computing per-sample and overall VCF QC statistics
Use GATK HaplotypeCaller instead when calling variants with local realignment in human samples
Use VCFtools instead for population genetics statistics (Fst, LD, Hardy-Weinberg)
Use bcftools in the HTSlib pipeline; use picard for duplicate-marking and library metrics
Prerequisites
Installation: bcftools 1.17+ (part of HTSlib suite with samtools)
Input requirements: VCF or BGzipped+tabix-indexed VCF (.vcf.gz + .vcf.gz.tbi) for region queries
Companion tools: samtools for BAM processing; tabix for VCF indexing
Check before installing: The tool may already be available in the current environment (e.g., inside a pixi / conda env). Run command -v bcftools first and skip the install commands below if it returns a path. When running inside a pixi project, invoke the tool via pixi run bcftools rather than bare bcftools.
# Bioconda (recommended — installs HTSlib suite)
conda install -c bioconda bcftools
# Homebrew (macOS)
brew install bcftools
# Verify
bcftools --version | head -1
# bcftools 1.20
# Index a VCF for region queries
bcftools index -t variants.vcf.gz # creates .tbi