albert-ying/autonomous-lab/variant-calling
Claude Code and agent skill by albert-ying/autonomous-lab
Trust tier 3
- community
Source check pending
Checking that the SKILL.md file is still in the repository.
Install
npx vskill@latest install albert-ying/autonomous-lab/variant-callingSKILL.md
Variant Calling Skill
When to Use
Use when calling SNPs and indels from aligned BAM files against a reference.
Standard Workflow
- Mark duplicates (optional):
samtools markdup - Call variants with freebayes:
freebayes -f reference.fasta -p 1 sample.bam > variants.vcf
OR with bcftools: bcftools mpileup -f ref.fa sample.bam | bcftools call -mv -Oz -o variants.vcf.gz
- Filter variants:
bcftools filter -s LowQual -e 'QUAL<20' variants.vcf
Key Decisions
- For haploid organisms (E. coli), use ploidy=1
- freebayes is good for bacterial genomes; bcftools is fast and reliable
- Filter on QUAL score and read depth
Security
- Security scanPassed, 90 of 100Pattern checks on the skill's files.
- Model reviewPassed
Quality evaluation
- Task evaluationNot runNo evaluation yet. Run one in Skill Studio.
Source
- SKILL.md in the repositoryChecking.autolab/acquired_skills/variant-calling/SKILL.md
Popularity
- 7-day trend score
- 5
Not refreshed yet.
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