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

HaplotypeCaller: data generated from amplicon sequencing 



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    Data like this usually deserves a different approach such as pileup. 

    I would strongly recommend using ABRA2 for SW realignment and freebayes or bcftools to capture variants. 

    HaplotypeCaller seems to take some more time to decide how to handle data like this one. 

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    joy bordini

    Hi Erika Salvi,


    I faced the same problem and i solved by setting

    --dont-use-soft-clipped-bases true
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