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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    Gökalp Çelik

    Hi RN Sarma

    We cannot directly act on your slurm job script however it may be better for you to run your individual files one by one to see how it goes and whether you receive any error messages during the run. 

    Default parameters of HaplotypeCaller should suffice for most germline diploid cases however if your organism has a different ploidy then you need to adjust those parameters accordingly. If your organism of interest is diploid then we suggest you to run HaplotypeCaller with default parameters to see what comes out. 

    You also need to pay attention to the experimental setup you have. Depending on the type of experiment ( whole genome short reads, long reads, amplicon targetted sequencing etc.) the number of variants you may catch differs therefore it is up to  your samples to provide that information to you. 

    I hope these help.


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