bio-gatk-variant-calling

npx skills add majiayu000/claude-skill-registry --skill gatk-variant-calling --agent claude-code

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

# GATK Variant Calling GATK HaplotypeCaller is the gold standard for germline variant calling. This skill covers the GATK Best Practices workflow. ## Prerequisites BAM files should be preprocessed: 1. Mark duplicates 2. Base quality score recalibration (BQSR) - optional but recommended ## Single-Sample Calling ### Basic HaplotypeCaller ```bash gatk HaplotypeCaller \ -R reference.fa \ -I sample.bam \ -O sample.vcf.gz ``` ### With Standard Annotations ```bash gatk HaplotypeCaller \ -R reference.fa \ -I sample.bam \ -O sample.vcf.gz \ -A Coverage \ -A QualByDepth \ -A FisherStrand \ -A StrandOddsRatio \ -A MappingQualityRankSumTest \ -A ReadPosRankSumTest ``` ### Target Intervals (Exome/Panel) ```bash gatk HaplotypeCaller \ -R reference.fa \ -I sample.bam \ -L targets.interval_list \ -O sample.vcf.gz ``` ### Adjust Calling Confidence ```bash gatk HaplotypeCaller \ -R reference.fa \ -I sample.bam \ -O sample.vcf.gz \ --standard-min-confidence-threshold-for-calling 20 ``` ## GVCF Workflow (Recommended for Cohorts) The GVCF workflow enables joint genotyping across samples for better variant calls. ### Step 1: Generate GVCFs per Sample ```bash gatk HaplotypeCaller \ -R reference.fa \ -I s

gatk HaplotypeCaller \
Create sample map file
sample1    /path/to/sample1.g.vcf.gz
sample2    /path/to/sample2.g.vcf.gz
gatk GenomicsDBImport \
gatk CombineGVCFs \
From GenomicsDB
gatk GenotypeGVCFs \
From combined GVCF
Build SNP model