bio-workflows-fastq-to-variants

npx skills add majiayu000/claude-skill-registry --skill fastq-to-variants --agent claude-code

Same command for any agent — swap --agent for codex, cursor, copilot.

# 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

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 \