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

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    when I use GATK tool HaplotypeCaller,I find a bug: When the two mutations are very close,The results are very inaccurate。It is mainly reflected in two aspects:

    (1)This may cause one of the mutations to be missed

    For this two mutation,only one was detected by GATK.

    (2)One of the very close mutations in the results is a false positive

    For example:These two mutations,mutations 1 is a false positive,mutations 2 is True positive,but the qual of this mutations 2 is also very low,just like mutations 1.This mutations  2 may result in being filtered。


    How can gatk avoid this situation?Thank you very much!

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