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Normalize indel representation and split multiallelic variants using bcftools norm.
Passed 21 of 22 test cases with the skill, and 15 of 22 without it.
and 5 more in the full report
7 fixed15 passed either way0 still failing1 broke
Tokens, turns and time describe resource use, not a dollar price.
One of 6 test cases the skill fixed. Same model, same prompt, with and without the skill.
I have a call set `variants.vcf.gz` containing both SNPs and indels. I want to split multiallelic SNP sites into separate biallelic records, but I want to leave multiallelic indel sites completely untouched. Which parameter flag should I pass when calling the normalization command?
| Checked | Without skill | With skill |
|---|---|---|
| The command uses the flag -m-snps. | Missed | Passed |
The instructions your model reads when the skill loads.
Left-align indels and split multiallelic sites using bcftools norm.
The same variant can be represented multiple ways:
# Same deletion, different representations
chr1 100 ATCG A (right-aligned)
chr1 100 ATC A (left-aligned, normalized)
chr1 101 TCG T (different position)
Normalization ensures consistent representation for:
bcftools norm -f reference.fa input.vcf.gz -Oz -o normalized.vcf.gz
test cases passed, vs 15 / 22 without
More skills from the same source and nearby in the registry, with their headline benchmark lift.