Merge, concatenate, sort, intersect, and subset VCF files using bcftools.
SkillScore96Maintained
Automatic
◆Data Engineer pack
Last verified 8/2/2026
What it changes
Passed 23 of 24 test cases with the skill, and 18 of 24 without it.
Without skill75%
With skill96%
Checks it passed that the model alone missed
Includes the --missing-to-ref option in the command.
Includes the -m option to enforce a memory restriction.
Outputs results directly to a file using the -w1 option.
and 2 more in the full report
5 fixed18 passed either way1 still failing0 broke
Pass-rate lift
+21 pp
Tokens
+118%
Agent turns
0%
Response time
-49%
Model gemini-3.6-flashMeasured 8/2/2026v123 of 24 cases passed with skill
Tokens, turns and time describe resource use, not a dollar price.
See it in action
One of 5 test cases the skill fixed. Same model, same prompt, with and without the skill.
1 of 5
Prompt
When using `bcftools isec` on two callsets, I want to select variants that are present in file 1 but NOT present in file 2 using the bitmask operator flag. What mask syntax represents file 1 AND NOT file 2?
What was checked, without and with the skill
Checked
Without skill
With skill
Uses the -n~10 flag to filter variants present in file 1 but absent in file 2.
Missed
Passed
case-19 · 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.md387 linessingle file
VCF Manipulation
Merge, concat, sort, and compare VCF files using bcftools.
Operations Overview
Operation
Command
Use Case
Merge
bcftools merge
Combine samples from multiple VCFs
Concat
bcftools concat
Combine regions from multiple VCFs
Sort
bcftools sort
Sort unsorted VCF
Intersect
bcftools isec
Compare/intersect call sets
Subset
bcftools view
Extract samples or regions
bcftools merge
Combine multiple VCF files with different samples at the same positions.