Comprehensive variant annotation using bcftools annotate/csq, VEP, SnpEff, and ANNOVAR. Add database annotations, predict functional consequences, and assess clinical significance.
SkillScore95Maintained
Automatic
◆Clinical / Healthcare pack
Last verified 8/2/2026
What it changes
Passed 21 of 22 test cases with the skill, and 17 of 22 without it.
Without skill77%
With skill95%
Checks it passed that the model alone missed
uses the --pick flag
uses the --everything flag
uses bcftools norm with the -m-any flag
and 4 more in the full report
4 fixed17 passed either way1 still failing0 broke
Pass-rate lift
+18 pp
Tokens
+131%
Agent turns
0%
Response time
-51%
Model gemini-3.6-flashMeasured 8/2/2026v121 of 22 cases passed with skill
Tokens, turns and time describe resource use, not a dollar price.
See it in action
One of 4 test cases the skill fixed. Same model, same prompt, with and without the skill.
1 of 4
Prompt
I have a BED file where the 4th column contains region names. I want to use bcftools to annotate my VCF with these region names into a new INFO field called REGION. I also need to provide the header line for this new INFO field directly in the command. What is the command?
What was checked, without and with the skill
Checked
Without skill
With skill
specifies the -c CHROM,FROM,TO,INFO/REGION flag
Passed
Passed
uses the -h flag with a string containing ##INFO=<ID=REGION,Number=1,Type=String,Description="Region name">
Missed
Passed
case-05 · gemini-3.6-flash · 8/2/2026 · answers are capped and redacted
What's inside
The instructions your model reads when the skill loads.
SKILL.md376 linessingle file
Variant Annotation
Tool Comparison
Tool
Best For
Speed
Output
bcftools csq
Simple consequence prediction
Fast
VCF
VEP
Comprehensive with plugins
Moderate
VCF/TXT
SnpEff
Fast batch annotation
Fast
VCF
ANNOVAR
Flexible databases
Moderate
TXT
bcftools annotate
Add Annotations from Database
bcftools annotate -a dbsnp.vcf.gz -c ID input.vcf.gz -Oz -o annotated.vcf.gz