Is bio-variant-calling safe to install?

SaferSkills independently audited bio-variant-calling (Agent Skill) and scored it 100/100 (green). The audit ran 55 deterministic rules across Security, Supply Chain, Maintenance, Transparency, and Community; it found 0 high-severity and 0 lower-severity findings. The full rule-by-rule trace and per-finding evidence are below. Free, methodology-open.

CategoryWeightCategory scoreContribution

Securityprompt, exec, net, exfil, eval

35%

100

35.0 pts

Supply chainhash, typosquat, maintainer, lockfile

20%

100

20.0 pts

Maintenancestaleness, pinning, CI

15%

100

15.0 pts

TransparencySKILL.md, perms, README

15%

100

15.0 pts

Communityinstalls, verify, response

15%

100

15.0 pts

Findings & checks · 0 flagged

Securityscore 100 · 0 findings

✓—All security checks passedNo findings in this category for the latest scan.pass

Supply chainscore 100 · 0 findings

✓—All supply chain checks passedNo findings in this category for the latest scan.pass

Maintenancescore 100 · 0 findings

✓—All maintenance checks passedNo findings in this category for the latest scan.pass

Transparencyscore 100 · 0 findings

✓—All transparency checks passedNo findings in this category for the latest scan.pass

Communityscore 100 · 0 findings

✓—All community checks passedNo findings in this category for the latest scan.pass

The primary manifest — the file an agent reads to learn what this artifact does.

skills/variant-interpretation-acmg/bioSkills/variant-calling/SKILL.md · 1 file

skills/variant-interpretation-acmg/bioSkills/variant-calling/SKILL.md6.0 KB · Markdown

name: bio-variant-calling

description: Call SNPs and indels from aligned reads using bcftools mpileup and call. Use when detecting variants from BAM files or generating VCF from alignments.

tool_type: cli

primary_tool: bcftools

measurable_outcome: Execute skill workflow successfully with valid output within 15 minutes.

allowed-tools:

- read_file

- run_shell_command

Variant Calling

Call SNPs and indels from aligned reads using bcftools.

Basic Workflow

BAM file + Reference FASTA
         |
         v
   bcftools mpileup (generate pileup)
         |
         v
   bcftools call (call variants)
         |
         v
   VCF file

bcftools mpileup + call

Basic Variant Calling

bcftools mpileup -f reference.fa input.bam | bcftools call -mv -o variants.vcf

Output Compressed VCF

bcftools mpileup -f reference.fa input.bam | bcftools call -mv -Oz -o variants.vcf.gz
bcftools index variants.vcf.gz

Call Specific Region

bcftools mpileup -f reference.fa -r chr1:1000000-2000000 input.bam | \
    bcftools call -mv -o region.vcf

Call from Multiple BAMs

bcftools mpileup -f reference.fa sample1.bam sample2.bam sample3.bam | \
    bcftools call -mv -o variants.vcf

BAM List File

# bams.txt: one BAM path per line
bcftools mpileup -f reference.fa -b bams.txt | bcftools call -mv -o variants.vcf

mpileup Options

Quality Filtering

bcftools mpileup -f reference.fa \
    -q 20 \           # Min mapping quality
    -Q 20 \           # Min base quality
    input.bam | bcftools call -mv -o variants.vcf

Annotate with Read Depth

bcftools mpileup -f reference.fa -a DP,AD input.bam | bcftools call -mv -o variants.vcf

Full Annotation Set

bcftools mpileup -f reference.fa \
    -a FORMAT/DP,FORMAT/AD,FORMAT/ADF,FORMAT/ADR,INFO/AD \
    input.bam | bcftools call -mv -o variants.vcf

Target Regions (BED)

bcftools mpileup -f reference.fa -R targets.bed input.bam | \
    bcftools call -mv -o variants.vcf

Max Depth

bcftools mpileup -f reference.fa -d 1000 input.bam | bcftools call -mv -o variants.vcf

call Options

Calling Models

Flag	Model	Use Case
`-m`	Multiallelic caller	Default, recommended
`-c`	Consensus caller	Legacy, single sample

Output Variants Only

bcftools mpileup -f reference.fa input.bam | bcftools call -mv -o variants.vcf
# -v outputs variant sites only (not reference calls)

Output All Sites

bcftools mpileup -f reference.fa input.bam | bcftools call -m -o all_sites.vcf
# Without -v, outputs all sites including reference

Ploidy

# Haploid calling
bcftools mpileup -f reference.fa input.bam | bcftools call -m --ploidy 1 -o variants.vcf

# Specify ploidy file
bcftools mpileup -f reference.fa input.bam | bcftools call -m --ploidy-file ploidy.txt -o variants.vcf

Prior Probability

# Adjust variant prior (default 1.1e-3)
bcftools mpileup -f reference.fa input.bam | bcftools call -m -P 0.001 -o variants.vcf

Common Pipelines

Standard SNP/Indel Calling

bcftools mpileup -Ou -f reference.fa \
    -q 20 -Q 20 \
    -a FORMAT/DP,FORMAT/AD \
    input.bam | \
bcftools call -mv -Oz -o variants.vcf.gz

bcftools index variants.vcf.gz

Multi-sample Calling

bcftools mpileup -Ou -f reference.fa \
    -a FORMAT/DP,FORMAT/AD \
    sample1.bam sample2.bam sample3.bam | \
bcftools call -mv -Oz -o cohort.vcf.gz

bcftools index cohort.vcf.gz

Calling with Regions

bcftools mpileup -Ou -f reference.fa \
    -R targets.bed \
    -a FORMAT/DP,FORMAT/AD \
    input.bam | \
bcftools call -mv -Oz -o targets.vcf.gz

Parallel by Chromosome

for chr in chr1 chr2 chr3; do
    bcftools mpileup -Ou -f reference.fa -r "$chr" input.bam | \
        bcftools call -mv -Oz -o "${chr}.vcf.gz" &
done
wait

# Concatenate results
bcftools concat -Oz -o all.vcf.gz chr*.vcf.gz
bcftools index all.vcf.gz

Annotation Tags

INFO Tags

Tag	Description
`DP`	Total read depth
`AD`	Allelic depths
`MQ`	Mapping quality
`FS`	Fisher strand bias
`SGB`	Segregation based metric

FORMAT Tags

Tag	Description
`GT`	Genotype
`DP`	Read depth per sample
`AD`	Allelic depths per sample
`ADF`	Forward strand allelic depths
`ADR`	Reverse strand allelic depths
`GQ`	Genotype quality
`PL`	Phred-scaled likelihoods

Request Specific Annotations

bcftools mpileup -f reference.fa \
    -a FORMAT/DP,FORMAT/AD,FORMAT/SP,INFO/AD \
    input.bam | bcftools call -mv -o variants.vcf

Performance Options

Multi-threading

bcftools mpileup -f reference.fa --threads 4 input.bam | \
    bcftools call -mv --threads 4 -o variants.vcf

Uncompressed BCF for Speed

bcftools mpileup -Ou -f reference.fa input.bam | bcftools call -mv -Ou | \
    bcftools filter -Oz -o filtered.vcf.gz

Quick Reference

Task	Command
Basic calling	`bcftools mpileup -f ref.fa in.bam \	bcftools call -mv -o out.vcf`
With quality filter	`bcftools mpileup -f ref.fa -q 20 -Q 20 in.bam \	bcftools call -mv`
Region	`bcftools mpileup -f ref.fa -r chr1:1-1000 in.bam \	bcftools call -mv`
Multi-sample	`bcftools mpileup -f ref.fa s1.bam s2.bam \	bcftools call -mv`
With annotations	`bcftools mpileup -f ref.fa -a DP,AD in.bam \	bcftools call -mv`

Common Errors

Error	Cause	Solution
`no FASTA reference`	Missing -f	Add `-f reference.fa`
`reference mismatch`	Wrong reference	Use same reference as alignment
`no variants called`	Low quality/depth	Lower quality thresholds

vcf-basics - View and query resulting VCF
filtering-best-practices - Filter variants by quality
variant-normalization - Normalize indels
alignment-files/pileup-generation - Alternative pileup generation

bio-variant-calling— agent skill

Is bio-variant-calling safe to install?

Variant Calling

Basic Workflow

bcftools mpileup + call

Basic Variant Calling

Output Compressed VCF

Call Specific Region

Call from Multiple BAMs

BAM List File

mpileup Options

Quality Filtering

Annotate with Read Depth

Full Annotation Set

Target Regions (BED)

Max Depth

call Options

Calling Models

Output Variants Only

Output All Sites

Ploidy

Prior Probability

Common Pipelines

Standard SNP/Indel Calling

Multi-sample Calling

Calling with Regions

Parallel by Chromosome

Annotation Tags

INFO Tags

FORMAT Tags

Request Specific Annotations

Performance Options

Multi-threading

Uncompressed BCF for Speed

Quick Reference

Common Errors

Audit the pieces. Scan the whole. Decide.

Is bio-variant-calling safe to install?

Variant Calling

Basic Workflow

bcftools mpileup + call

Basic Variant Calling

Output Compressed VCF

Call Specific Region

Call from Multiple BAMs

BAM List File

mpileup Options

Quality Filtering

Annotate with Read Depth

Full Annotation Set

Target Regions (BED)

Max Depth

call Options

Calling Models

Output Variants Only

Output All Sites

Ploidy

Prior Probability

Common Pipelines

Standard SNP/Indel Calling

Multi-sample Calling

Calling with Regions

Parallel by Chromosome

Annotation Tags

INFO Tags

FORMAT Tags

Request Specific Annotations

Performance Options

Multi-threading

Uncompressed BCF for Speed

Quick Reference

Common Errors

Related Skills

Audit the pieces. Scan the whole. Decide.