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

calling Multi-allelic single nucleotide variants with mutect2


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    Anton Kovalsky

    Hi paruchuri anoosha, thanks for your question, could you please provide IGV screenshots where you observe the expected variant sorted by base, the allele counts reported by IGV, and a description of the intervals bed file (how big are the intervals?; are they padded?) 

    We also recommend that you use the PoN and Germline resource from our best practices bucket

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