bio-workflows-fastq-to-variants
End-to-end DNA sequencing workflow from FASTQ files to variant calls. Covers QC, alignment with BWA, BAM processing, and variant calling with bcftools or GATK HaplotypeCaller. Use when calling variants from raw sequencing reads.
npx skills add majiayu000/claude-skill-registry --skill fastq-to-variants-gptomics-bioskills --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# FASTQ to Variants Workflow Complete pipeline from raw DNA sequencing FASTQ files to filtered variant calls. ## Workflow Overview ``` FASTQ files | v [1. QC & Trimming] -----> fastp | v [2. Alignment] ---------> bwa-mem2 | v [3. BAM Processing] ----> sort, markdup, index | v [4. Variant Calling] ---> bcftools (primary) or GATK | v [5. Filtering] ---------> Quality filters | v Filtered VCF ``` ## Primary Path: BWA + bcftools ### Step 1: Quality Control with fastp ```bash # Single sample fastp -i sample_R1.fastq.gz -I sample_R2.fastq.gz \ -o sample_R1.trimmed.fq.gz -O sample_R2.trimmed.fq.gz \ --detect_adapter_for_pe \ --qualified_quality_phred 20 \ --length_required 50 \ --html sample_fastp.html # Batch processing for sample in sample1 sample2 sample3; do fastp -i ${sample}_R1.fastq.gz -I ${sample}_R2.fastq.gz \ -o trimmed/${sample}_R1.fq.gz -O trimmed/${sample}_R2.fq.gz \ --detect_adapter_for_pe \ --html qc/${sample}_fastp.html done ``` **QC Checkpoint 1:** Check fastp reports - Q30 bases >85% (DNA typically higher quality than RNA) - Adapter content <1% - No unusual GC distribution ### Step 2: BWA-MEM2 Alignment ```bash # Index reference (once) bwa-mem2 index reference.fa # Align
- Workflow Overview
- Primary Path: BWA + bcftools
- Step 1: Quality Control with fastp
- Step 2: BWA-MEM2 Alignment
- Step 3: BAM Processing
- Step 4: Variant Calling with bcftools
- Step 5: Variant Filtering
- Alternative Path: BWA + GATK HaplotypeCaller
- Step 4 Alternative: GATK Variant Calling
- Step 5 Alternative: GATK Variant Filtering
- Parameter Recommendations
- Choosing Between bcftools and GATK
- Troubleshooting
- Complete Pipeline Script
Single sample
fastp -i sample_R1.fastq.gz -I sample_R2.fastq.gz \
Batch processing
for sample in sample1 sample2 sample3; do
fastp -i ${sample}_R1.fastq.gz -I ${sample}_R2.fastq.gz \
done
Index reference (once)
bwa-mem2 index reference.fa
Align with read group info
bwa-mem2 mem -t 8 \What does the bio-workflows-fastq-to-variants skill do?
End-to-end DNA sequencing workflow from FASTQ files to variant calls. Covers QC, alignment with BWA, BAM processing, and variant calling with bcftools or GATK HaplotypeCaller. Use when calling variants from raw sequencing reads.
How do I install it?
Run `npx skills add majiayu000/claude-skill-registry --skill fastq-to-variants-gptomics-bioskills --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From majiayu000/claude-skill-registry, a repository with 534 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.