Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Why does GATK haplotype caller calls SNPs from soft-clipped bases?

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    Genevieve Brandt

    Hello AlibiKr, we do not support GATK3 anymore. Please re-run these commands with GATK4 and let us know if the issue persists. 

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