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bio-gatk-variant-calling

separate

Variant calling with GATK HaplotypeCaller following best practices. Covers germline SNP/indel calling, GVCF workflow for cohorts, joint genotyping, and variant quality score recalibration (VQSR). Use when calling variants with GATK HaplotypeCaller.

When to use

• germline SNP/indel calling
• GVCF workflow for cohorts
• joint genotyping
• variant quality score recalibration (VQSR)
• calling variants with GATK HaplotypeCaller
• hard filtering for small datasets

When not to use

• somatic variant calling
• non-germline variant calling

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