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Generate variant statistics, sample concordance, and quality metrics using bcftools stats and gtcheck.
Passed 21 of 22 test cases with the skill, and 19 of 22 without it.
2 fixed19 passed either way1 still failing0 broke
Tokens, turns and time describe resource use, not a dollar price.
One of 2 test cases the skill fixed. Same model, same prompt, with and without the skill.
I have a callset `variants.vcf.gz` and want to inspect basic summary statistics such as record counts and SNP totals without viewing individual site lines or full per-sample breakdowns. What line prefix filter should I extract from the command-line statistics output?
| Checked | Without skill | With skill |
|---|---|---|
| Filters output for lines starting with ^SN | Passed | Passed |
| Strips leading table formatting to isolate summary field values | Missed | Passed |
The instructions your model reads when the skill loads.
Generate statistics and quality metrics using bcftools.
| Command | Purpose |
|---|---|
bcftools stats | Comprehensive variant statistics |
bcftools gtcheck | Sample concordance and relatedness |
bcftools query | Custom summaries |
bcftools stats input.vcf.gz > stats.txt
bcftools stats input.vcf.gz | grep "^SN"
Output sections:
test cases passed, vs 19 / 22 without
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