vcf-variant-filtering

95 / 100 · Low risk

Fine to try.

By BioTender-max/awesome-bio-agent-skills (GitHub) · design · 219 stars · scanned at commit 8cbdd18

Guide to quality filtering raw VCF files before computing summary stats (Ts/Tv ratio, variant counts, AF distributions). Covers detecting raw VCFs via FILTER column and QUAL inspection, QUAL-based filtering with bcftools, Ts/Tv interpretation, and when NOT to filter. Read before any variant-level QC task. See bcftools-variant-manipulation for advanced filters, gatk-variant-calling for caller config, samtools-bam-processing for upstream alignment QC.

Works with any agent that supports SKILL.md skills.

What this skill can do

Runs commands on your computer

The author does not mention this.

Found in 8 places.

skills/sciagent/vcf-variant-filtering/SKILL.md, line 71bcftools query -f '%FILTER\n' input.vcf | sort | uniq -c | sort -rn | head
skills/sciagent/vcf-variant-filtering/SKILL.md, line 118bcftools stats input.vcf | grep ^TSTV
skills/sciagent/vcf-variant-filtering/SKILL.md, line 132bcftools view -i 'QUAL>=30' input.vcf | bcftools stats - > filtered_stats.txt

Show 5 more

skills/sciagent/vcf-variant-filtering/SKILL.md, line 170bcftools view -h input.vcf | grep -E '##(FILTER|source|GATKCommandLine|bcftools)'
skills/sciagent/vcf-variant-filtering/SKILL.md, line 181bcftools query -f '%QUAL\n' input.vcf | awk '{if($1<30) low++; else high++} END {print "QUAL<30:", low+0, "QUAL>=30:", high+0}'
skills/sciagent/vcf-variant-filtering/SKILL.md, line 191bcftools view -i 'QUAL>=30' input.vcf -Oz -o filtered.vcf.gz
skills/sciagent/vcf-variant-filtering/SKILL.md, line 200bcftools view -i 'QUAL>=30' input.vcf | bcftools stats - | grep ^TSTV | cut -f5
skills/sciagent/vcf-variant-filtering/SKILL.md, line 214bcftools view -H input.vcf | wc -l

Install

Paste this into your terminal. It downloads exactly the version we scanned, not whatever is newest.

if [ -e ~/.agents/skills/'vcf-variant-filtering' ] || [ -L ~/.agents/skills/'vcf-variant-filtering' ]; then echo 'A skill folder named vcf-variant-filtering already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/BioTender-max/awesome-bio-agent-skills' "$d" && git -C "$d" checkout --quiet '8cbdd18837aa6296c4e77616a03b323bd69b57b1' -- 'skills/sciagent/vcf-variant-filtering' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/sciagent/vcf-variant-filtering' ~/.agents/skills/'vcf-variant-filtering' && rm -rf "$d"; fi

Codex reads ~/.agents/skills directly. For Claude Code, Cursor, Copilot, Gemini CLI, Antigravity or OpenCode, also link it. For Claude Code: ln -s ~/.agents/skills/'vcf-variant-filtering' ~/.claude/skills/'vcf-variant-filtering' (other agents: ~/.cursor/skills, ~/.copilot/skills, ~/.gemini/skills, ~/.gemini/config/skills, ~/.config/opencode/skills). Or install through the finder skill, which does both.

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Score history

Date	Version	Score
2026-11-07	`8cbdd18`	95