bio-consensus-sequences

95 / 100 · Low risk

Fine to try.

By lilinji/GeneTind-Life-Skills (GitHub) · other · 17 stars · scanned at commit 908229c

Generate consensus FASTA sequences by applying VCF variants onto a reference with bcftools consensus, or build viral/amplicon consensus with iVar. Use when reconstructing a sample-specific reference or haplotype, deciding -H haplotype vs IUPAC vs all-ALT projection, masking no-coverage sites so a consensus does not manufacture false reference calls, or setting iVar min-depth/min-frequency policy for surveillance genomes.

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 12 places.

skills/bio-consensus-sequences/SKILL.md, line 43bcftools index input.vcf.gz # .csi index (or tabix -p vcf)
skills/bio-consensus-sequences/SKILL.md, line 51bcftools query -l input.vcf.gz # list samples
skills/bio-consensus-sequences/SKILL.md, line 58bcftools consensus -f reference.fa -r chr1:1000000-1010000 -s sample1 input.vcf.gz > gene.fa

Show 9 more

skills/bio-consensus-sequences/SKILL.md, line 76bcftools query -f '%CHROM\t%POS[\t%GT]\n' input.vcf.gz | head # phased: 0|1 ; unphased: 0/1
skills/bio-consensus-sequences/SKILL.md, line 100bcftools view -i 'GT="AA"' input.vcf.gz | bcftools consensus -f reference.fa > hom_alt.fa
skills/bio-consensus-sequences/SKILL.md, line 112samtools depth -a aligned.bam | awk '$3 < 10 {print $1"\t"$2-1"\t"$2}' | bedtools merge > lowcov.bed
skills/bio-consensus-sequences/SKILL.md, line 128bcftools norm -f reference.fa input.vcf.gz -Oz -o norm.vcf.gz
skills/bio-consensus-sequences/SKILL.md, line 136bcftools consensus -f reference.fa norm.vcf.gz 2>&1 >consensus.fa | grep -i 'overlap\|warn'
skills/bio-consensus-sequences/SKILL.md, line 146ivar trim -b primers.bed -p trimmed -i aligned.bam
skills/bio-consensus-sequences/SKILL.md, line 167bcftools view -f PASS input.vcf.gz -Oz -o pass.vcf.gz && bcftools index pass.vcf.gz
skills/bio-consensus-sequences/SKILL.md, line 180bcftools consensus -f reference.fa -c chain.txt -p "sample1_" input.vcf.gz > consensus.fa
skills/bio-consensus-sequences/SKILL.md, line 203minimap2 -a reference.fa consensus.fa | samtools view -b -o aln.bam # inspect where it diverges

Install

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

if [ -e ~/.agents/skills/'bio-consensus-sequences' ] || [ -L ~/.agents/skills/'bio-consensus-sequences' ]; then echo 'A skill folder named bio-consensus-sequences already exists — not replacing it' >&2; false; else d=$(mktemp -d) && git clone --quiet --filter=blob:none --no-checkout 'https://github.com/lilinji/GeneTind-Life-Skills' "$d" && git -C "$d" checkout --quiet '908229c955510a1841b216e8bf58f6b22818d4dc' -- 'skills/bio-consensus-sequences' && mkdir -p ~/.agents/skills && cp -R "$d"/'skills/bio-consensus-sequences' ~/.agents/skills/'bio-consensus-sequences' && 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/'bio-consensus-sequences' ~/.claude/skills/'bio-consensus-sequences' (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
2026-11-11	`908229c`	95