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

Mutect2 -could not detect expected Indels



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    Gökalp Çelik

    Hi Shivangi Agarwal

    Mutect2 and HaplotypeCaller of GATK utilizes local reassembly for genotyping of variants and the default parameters of both tools are mostly optimized for whole genome and exome sequencing samples and therefore may not be enough for other special NGS data types such as amplicon sequencing. Depth of data may also be an issue for some variants however these tools have bunch of parameters for tuning for those cases and some of the most useful parameters are summarized in the following article 

    Can you try some of the recommended tunable parameters and let us know whether that works for you? 


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    Shivangi Agarwal

    Okay, thanks. I am looking into it and will get back to you soon.






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