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

6 comments

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    Andrew Zhang

    Not  a googlable question....

     

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    Bhanu Gandham

    Hi Andrew Zhang

     

    CRSP is the Broad Clinical Research Sequencing Platform. It was developed since they needed it and we made it available as part of the Mutect2 validation tools.

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    Andrew Zhang

    Hello Bhanu

    Many thanks,I am wondering is it necessary to remove nearby INDEL,when I was trying to get the de novo  mutation using HaplotypeCaller.

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    Bhanu Gandham

    Hi Andrew,

     

    Depends on your experimental design and what it is that you are trying to do. Can you explain that a little more?

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    Andrew Zhang

    Hi Bhanu,

    It is to use the candidate list currently obtained through the VCF file of the parents and child. Then through some reasonable steps, reduce the false positive rate of spontaneous mutations, thereby reducing the workload of subsequent experimental verification.

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    Bhanu Gandham

    Hi Andrew Zhang

     

    We do not recommend using this tool. This was developed for a very specific internal purposes only. 

     

    Going forward we are going to make it very clear in our documentation that this is not for external use.

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